![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10106 closed defect (can't reproduce)
MemoryError saving session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/CSLiao/Desktop/HW3.cxs
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at level
0.07, step 2, values float32
Opened 8hfr map 10 as #3, grid size 109,89,102, pixel 3.33, shown at level
0.102, step 1, values float32
Opened emdb 34638 as #6, grid size 400,400,400, pixel 1.34, shown at level
0.07, step 2, values float32
Opened 34638_clean as #11, grid size 400,400,400, pixel 1.34, shown at level
0.05, step 2, values float32
Opened 34725_clean as #12, grid size 800,800,800, pixel 0.668, shown at level
0.09, step 2, values float32
Opened emdb 34640 as #7, grid size 320,320,320, pixel 0.668, shown at level
0.1, step 2, values float32
Opened 34638_clean 0 as #13.1, grid size 400,400,400, pixel 1.34, shown at
level 0.06, step 1, values float32
Opened 34638_clean 2 as #13.3, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 3 as #13.4, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 4 as #13.5, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 5 as #13.6, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 6 as #13.7, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 7 as #13.8, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 8 as #13.9, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 9 as #13.10, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 10 as #13.11, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 11 as #13.12, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 12 as #13.13, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 13 as #13.14, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 14 as #13.15, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 15 as #13.16, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 16 as #13.17, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 17 as #13.18, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 19 as #13.20, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 20 as #13.21, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened emdb 35767 as #10, grid size 800,800,800, pixel 0.668, shown at level
0.1, step 2, values float32
Log from Tue Nov 7 17:16:20 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/CSLiao/Desktop/HW1.cxs
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at level
0.195, step 1, values float32
Opened 8hfr map 10 as #3, grid size 109,89,102, pixel 3.33, shown at level
0.102, step 1, values float32
Opened volume difference as #4, grid size 800,800,800, pixel 0.668, shown at
level 0.185, step 1, values float32
Log from Mon Nov 6 16:34:47 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open emdb:34638 format ccp4 fromDatabase emdb
Opened emdb 34638 as #1, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> volume #1 level 0.08785
> volume #1 level 0.0944
> volume #1 level 0.1141
> volume #1 style image
> volume #1 level -0.04118,0 level 0.08766,0.8 level 2.95,1
> volume #1 level -0.04118,0 level 0.04835,0.7692 level 2.95,1
> volume #1 style mesh
> volume #1 level 0.1927
> volume #1 style image maximumIntensityProjection true
> volume #1 region 0,0,198,399,399,198 step 1 maximumIntensityProjection false
> showOutlineBox true
> volume #1 region 0,0,0,399,399,399 step 2
> volume #1 region 0,0,0,399,399,399 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 199,199,199 imageMode orthoplanes
> volume #1 imageMode "box faces"
> volume #1 level -0.04118,0 level 0.03108,0.5692 level 2.95,1
> volume #1 level -0.04118,0 level 0.1001,0.7385 level 2.95,1
> volume #1 region 0,0,0,399,399,399 step 2 colorMode auto8 imageMode "tilted
> slab" tiltedSlabAxis -0.1402,0.5655,0.8127 tiltedSlabOffset 302.4
> tiltedSlabSpacing 1.336 tiltedSlabPlaneCount 40
> volume #1 style surface
> volume #1 level 0.1141
> close #1
> open emdb:0220
Summary of feedback from opening 0220 fetched from emdb
---
note | Fetching compressed map 0220 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0220/map/emd_0220.map.gz
Opened emdb 0220 as #1, grid size 140,140,140, pixel 2.55, shown at level
0.0901, step 1, values float32
> open emdb:0369
Summary of feedback from opening 0369 fetched from emdb
---
note | Fetching compressed map 0369 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0369/map/emd_0369.map.gz
Opened emdb 0369 as #2, grid size 384,384,384, pixel 1.1, shown at level
0.0258, step 2, values float32
> hide #!1 models
> show cartoons
> hide atoms
> volume #2 tiltedSlabAxis 0.5945,0.7836,0.1802 tiltedSlabOffset 314.1
[Repeated 1 time(s)]
> volume #2 style mesh
> volume #2 style image region 0,0,190,383,383,190 step 1 imageMode "full
> region"
> volume #2 region 0,0,0,383,383,383 step 2
> volume #2 region 0,0,0,383,383,383 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 191,191,191 imageMode orthoplanes
> volume #2 style surface
> volume #2 change image level -0.007442,0 level 0.04754,0.8 level 0.1295,1
> volume #2 level 0.02207
> volume #2 level 0.02812
> open emdb:0370
Summary of feedback from opening 0370 fetched from emdb
---
note | Fetching compressed map 0370 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0370/map/emd_0370.map.gz
Opened emdb 0370 as #3, grid size 384,384,384, pixel 1.1, shown at level
0.0282, step 2, values float32
> open emdb:8346
Summary of feedback from opening 8346 fetched from emdb
---
note | Fetching compressed map 8346 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-8346/map/emd_8346.map.gz
Opened emdb 8346 as #4, grid size 256,256,256, pixel 1.62, shown at level
0.472, step 1, values float32
> open emdb:34725
Opened emdb 34725 as #5, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> hide #!2 models
> hide #!3 models
> hide #!4 models
> volume #5 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #5 region 0,0,0,799,799,799
[Repeated 9 time(s)]
> open emdb:34640
Summary of feedback from opening 34640 fetched from emdb
---
note | Fetching compressed map 34640 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34640/map/emd_34640.map.gz
Opened emdb 34640 as #6, grid size 320,320,320, pixel 0.668, shown at level
0.105, step 2, values float32
> open emdb:34638
Opened emdb 34638 as #7, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> open emdb:35767
Summary of feedback from opening 35767 fetched from emdb
---
note | Fetching compressed map 35767 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35767/map/emd_35767.map.gz
Opened emdb 35767 as #8, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> open emdb:34641
Summary of feedback from opening 34641 fetched from emdb
---
note | Fetching compressed map 34641 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34641/map/emd_34641.map.gz
Opened emdb 34641 as #9, grid size 320,320,320, pixel 0.668, shown at level
0.373, step 2, values float32
> open emdb:35812
Summary of feedback from opening 35812 fetched from emdb
---
note | Fetching compressed map 35812 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35812/map/emd_35812.map.gz
Opened emdb 35812 as #10, grid size 256,256,256, pixel 0.668, shown at level
0.154, step 1, values float32
> close #1-10
> open 3NC1
Summary of feedback from opening 3NC1 fetched from pdb
---
note | Fetching compressed mmCIF 3nc1 from
http://files.rcsb.org/download/3nc1.cif
3nc1 title:
Crystal structure of the CRM1-RanGTP complex [more info...]
Chain information for 3nc1 #1
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
Non-standard residues in 3nc1 #1
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> open 1JF5
Summary of feedback from opening 1JF5 fetched from pdb
---
notes | Fetching compressed mmCIF 1jf5 from
http://files.rcsb.org/download/1jf5.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
1jf5 title:
Crystal structure of thermoactinomyces vulgaris R-47 α-amylase 2 mutant F286A
[more info...]
Chain information for 1jf5 #2
---
Chain | Description | UniProt
A B | ALPHA AMYLASE II | NEPU2_THEVU 1-585
Non-standard residues in 1jf5 #2
---
CA — calcium ion
> open 6N8K
Summary of feedback from opening 6N8K fetched from pdb
---
notes | Fetching compressed mmCIF 6n8k from
http://files.rcsb.org/download/6n8k.cif
Fetching CCD GTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GTP/GTP.cif
6n8k title:
Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal
subunit [more info...]
Chain information for 6n8k #3
---
Chain | Description | UniProt
1 | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA |
2 | 5S rRNA |
3 | 5.8S rRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
o | 60S ribosomal protein L29 | RL29_YEAST 1-59
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
s | Ribosomal Protein uL1 |
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 6n8k #3
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> hide #!2 models
> hide #!1 models
> show #!3 atoms
> show #!3 cartoons
> show #!3 surfaces
> open 6N8K format mmcif fromDatabase pdb
6n8k title:
Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal
subunit [more info...]
Chain information for 6n8k #4
---
Chain | Description | UniProt
1 | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA |
2 | 5S rRNA |
3 | 5.8S rRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
o | 60S ribosomal protein L29 | RL29_YEAST 1-59
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
s | Ribosomal Protein uL1 |
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 6n8k #4
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> style #!3-4 ball
Changed 265642 atom styles
> hide #!3-4 atoms
> show #!3-4 cartoons
> hide #!3 models
> select add #4
132821 atoms, 142688 bonds, 3022 pseudobonds, 10922 residues, 4 models
selected
> close #1-3
> log metadata #4
Metadata for 6n8k #4
---
Title | Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S
ribosomal subunit
Citation | Zhou, Y., Musalgaonkar, S., Johnson, A.W., Taylor, D.W. (2019).
Tightly-orchestrated rearrangements govern catalytic center assembly of the
ribosome. Nat Commun, 10, 958-958. PMID: 30814529. DOI:
10.1038/s41467-019-08880-0
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)
CryoEM Map | EMDB 0370 — open map
Experimental method | Electron microscopy
Resolution | 3.6Å
> log chains #4
Chain information for 6n8k #4
---
Chain | Description | UniProt
1 | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA |
2 | 5S rRNA |
3 | 5.8S rRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
o | 60S ribosomal protein L29 | RL29_YEAST 1-59
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
s | Ribosomal Protein uL1 |
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> sequence chain #4/v
Alignment identifier is 4/v
> select /y:2-243
1826 atoms, 1848 bonds, 242 residues, 1 model selected
> hide all
> hide #4
> hide ~: sel
> hide
> hide #!4 target m
> show sel cartoons
> show #!4 models
> view sel
> hide 6n8k
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 6n8k cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide cartoons 6n8k
Expected ',' or a keyword
> open 5FL8
Summary of feedback from opening 5FL8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
note | Fetching compressed mmCIF 5fl8 from
http://files.rcsb.org/download/5fl8.cif
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> hide #!4 models
> select add #4
132821 atoms, 142688 bonds, 3022 pseudobonds, 10922 residues, 4 models
selected
> select subtract #4
Nothing selected
> open 5FL8 format mmcif fromDatabase pdb
Summary of feedback from opening 5FL8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #2
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> hide #!2 models
> show #!1 atoms
> show #!1 cartoons
> open 4wwu
Summary of feedback from opening 4wwu fetched from pdb
---
notes | Fetching compressed mmCIF 4wwu from
http://files.rcsb.org/download/4wwu.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
4wwu title:
Structure of Mex67:Mtr2 [more info...]
Chain information for 4wwu #3
---
Chain | Description | UniProt
A B D E G H J K | mRNA export factor MEX67 | MEX67_YEAST 1-487
C F I L | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
Non-standard residues in 4wwu #3
---
ZN — zinc ion
4wwu mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 5fl8
Summary of feedback from opening 5fl8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #5
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> open 5fl8 format mmcif fromDatabase pdb
Summary of feedback from opening 5fl8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #6
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> close #1-6
> close #
Expected a models specifier or a keyword
> open 4wwu format mmcif fromDatabase pdb
4wwu title:
Structure of Mex67:Mtr2 [more info...]
Chain information for 4wwu #1
---
Chain | Description | UniProt
A B D E G H J K | mRNA export factor MEX67 | MEX67_YEAST 1-487
C F I L | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
Non-standard residues in 4wwu #1
---
ZN — zinc ion
4wwu mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #1
> open 5FL8 format mmcif fromDatabase pdb
Summary of feedback from opening 5FL8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> open 5fl8 format mmcif fromDatabase pdb
Summary of feedback from opening 5fl8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #2
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> close #1
> open 5fl8 format mmcif fromDatabase pdb
Summary of feedback from opening 5fl8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> log metadata #1
Metadata for 5fl8 #1
---
Title | Cryo-em structure of the RIX1-REA1 pre-60S particle
Citation | Barrio-Garcia, C., Thoms, M., Flemming, D., KAter, L.,
Berninghausen, O., Bassler, J., Beckmann, R., Hurt, E. (2016). Architecture of
the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Nat.Struct.Mol.Biol., 23, 37-44. PMID: 26619264. DOI: 10.1038/nsmb.3132
Sources (natural) | Saccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (baker's yeast)
Saccharomyces cerevisiae (baker's yeast)
Experimental method | Electron microscopy
Resolution | 9.5Å
> log chains #1
Chain information for 5fl8 #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> log metadata #1
Metadata for 5fl8 #1
---
Title | Cryo-em structure of the RIX1-REA1 pre-60S particle
Citation | Barrio-Garcia, C., Thoms, M., Flemming, D., KAter, L.,
Berninghausen, O., Bassler, J., Beckmann, R., Hurt, E. (2016). Architecture of
the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Nat.Struct.Mol.Biol., 23, 37-44. PMID: 26619264. DOI: 10.1038/nsmb.3132
Sources (natural) | Saccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (baker's yeast)
Saccharomyces cerevisiae (baker's yeast)
Experimental method | Electron microscopy
Resolution | 9.5Å
> log chains #1
Chain information for 5fl8 #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> close #2
> hide atoms
> show cartoons
> nucleotides stubs
> nucleotides atoms
> style nucleic stick
Changed 65401 atom styles
> color bynucleotide
[Repeated 1 time(s)]
> select add #1
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 65401 atom styles
> nucleotides sel ladder
> color sel bynucleotide
> sequence chain #1/z
Alignment identifier is 1/z
> select #1/z:1-121
2576 atoms, 2880 bonds, 61 pseudobonds, 121 residues, 2 models selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 2576 atom styles
> view sel
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2576 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> hide #!1 models
> show #!1 models
> select add #1
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> select subtract #1
Nothing selected
> close #1
> help help:quickstart
> open emdb34725
'emdb34725' has no suffix
> open emdb:34725
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> open emdb:34638
Opened emdb 34638 as #2, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> open emdb:34725 format ccp4 fromDatabase emdb
Opened emdb 34725 as #3, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> close #1-3
> open emdb:34638
Opened emdb 34638 as #1, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #1
2 models selected
> close #1
> open emdb:34725
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #1 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #1 change image level -0.04277,0 level 0.2825,0.8 level 1.288,1
> volume #1 level 0.1256
> volume #1 region 0,0,0,799,799,799
> ui mousemode right "rotate selected models"
> open emdb:0220
Opened emdb 0220 as #2, grid size 140,140,140, pixel 2.55, shown at level
0.0901, step 1, values float32
> hide #!1 models
> volume #2 style mesh
> volume #2 style image
> volume #2 region 0,0,69,139,139,69 step 1 showOutlineBox true
> volume #2 region 0,0,80,139,139,80
> ui mousemode right rotate
[Repeated 1 time(s)]
> volume #2 region 0,0,0,139,139,139 step 1
> volume #2 style surface region 0,0,0,139,139,139 step 1
> volume #2 change image level -0.00914,0 level 0.09012,0.8 level 0.1297,1
> volume #2 level 0.08925
> show #!1 models
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,96.227,0,1,0,54.208,0,0,1,77.809
> ui mousemode right "rotate selected models"
> select add #2
3 models selected
> view matrix models
> #2,0.28099,0.37103,0.88509,1.0369,0.88907,0.24664,-0.38565,98.504,-0.36139,0.89527,-0.26057,206.6
> view matrix models
> #2,-0.78036,-0.31271,0.54153,371.2,-0.54273,-0.09149,-0.83491,491.8,0.31063,-0.94543,-0.098324,384.96
> view matrix models
> #2,-0.91048,-0.31539,0.2675,443.3,-0.28762,0.018157,-0.95757,448.9,0.29715,-0.94879,-0.10725,389.53
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.91048,-0.31539,0.2675,471.75,-0.28762,0.018157,-0.95757,479.9,0.29715,-0.94879,-0.10725,397.74
> view matrix models #1,1,0,0,-110.71,0,1,0,-129.09,0,0,1,-113.53
> view matrix models
> #2,-0.91048,-0.31539,0.2675,471.7,-0.28762,0.018157,-0.95757,479.51,0.29715,-0.94879,-0.10725,394.32
> view matrix models
> #2,-0.91048,-0.31539,0.2675,488.9,-0.28762,0.018157,-0.95757,501.11,0.29715,-0.94879,-0.10725,426.96
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.47931,0.87753,-0.013993,250.96,-0.87746,-0.47882,0.02836,518.99,0.018187,0.025872,0.9995,107.52
> view matrix models
> #2,-0.47496,0.87864,0.049101,238.81,-0.87956,-0.47218,-0.058524,533.58,-0.028237,-0.070983,0.99708,133.34
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-86.557,0,1,0,-107.03,0,0,1,-20.782
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.49312,0.86898,0.041267,245.13,-0.86962,-0.49103,-0.051544,533.92,-0.024527,-0.061304,0.99782,130.84
> select add #1
6 models selected
> hide #!2 models
> select add #2
6 models selected
> select add #2
6 models selected
> show #!2 models
> select add #2
6 models selected
> select add #2
6 models selected
> select add #2
6 models selected
> select add #2
6 models selected
> select add #2
6 models selected
> select add #1
6 models selected
> select add #1
6 models selected
> select add #2
6 models selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-86.472,0,1,0,-106.95,0,0,1,-20.545,#2,-0.49312,0.86898,0.041267,245.22,-0.86962,-0.49103,-0.051544,534,-0.024527,-0.061304,0.99782,131.08
> ui mousemode right select
> select clear
> select add #1
3 models selected
Drag select of 1 emdb 34725
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-16.73,0,1,0,-35.334,0,0,1,51.389
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.45648,0.76651,-0.45176,41.335,0.86557,-0.5001,0.026086,132.5,-0.20593,-0.40294,-0.89176,719.34
> view matrix models
> #1,0.60669,0.47856,-0.63475,127.99,0.75127,-0.60618,0.26104,128.27,-0.25984,-0.63524,-0.72729,751.93
> ui mousemode right "move picked models"
> view matrix models
> #1,0.60669,0.47856,-0.63475,34.505,0.75127,-0.60618,0.26104,37.427,-0.25984,-0.63524,-0.72729,527.9
> close #2
> view matrix models
> #1,0.60669,0.47856,-0.63475,127.67,0.75127,-0.60618,0.26104,130.66,-0.25984,-0.63524,-0.72729,684.42
> open 8HFR
8hfr title:
NPC-trapped pre-60S particle [more info...]
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 8hfr #2
---
MG — magnesium ion
> view matrix models
> #1,0.60669,0.47856,-0.63475,120.2,0.75127,-0.60618,0.26104,123.62,-0.25984,-0.63524,-0.72729,660.87
> ui mousemode right "move picked models"
> view matrix models
> #1,0.60669,0.47856,-0.63475,174.5,0.75127,-0.60618,0.26104,169.46,-0.25984,-0.63524,-0.72729,962.72
> view matrix models #2,1,0,0,-28.754,0,1,0,-28.701,0,0,1,-50.08
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.88085,0.4655,-0.086138,-40.775,0.43957,-0.87179,-0.21623,450.36,-0.17575,0.1526,-0.97254,794.66
> select add #1
3 models selected
> ui mousemode right select
> select clear
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.83899,0.24046,-0.48813,82.638,0.039766,0.86757,0.49572,-137.6,0.54269,-0.43532,0.71832,-7.513
> view matrix models
> #2,0.16681,-0.88874,-0.42698,526.95,0.14475,0.45043,-0.881,306.26,0.97531,0.085159,0.20378,-115.08
> select subtract #2
Nothing selected
> select add #1
3 models selected
> view matrix models
> #1,0.67368,0.58642,-0.44974,78.476,0.23935,-0.74889,-0.61796,577.44,-0.69919,0.30866,-0.64487,802.99
> view matrix models
> #1,-0.098366,0.87703,-0.47027,209.19,-0.58118,-0.43422,-0.68824,727.75,-0.80781,0.20561,0.55243,539.25
> view matrix models
> #1,0.8655,0.47862,-0.14778,-23.781,0.42666,-0.85896,-0.2831,468.18,-0.26244,0.18197,-0.94764,802.94
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.8655,0.47862,-0.14778,-51.59,0.42666,-0.85896,-0.2831,440.54,-0.26244,0.18197,-0.94764,751.56
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.86909,0.43029,0.24399,-144.27,0.40865,-0.9025,0.136,344.96,0.27872,-0.018494,-0.96019,666.28
> view matrix models
> #1,0.75002,0.54835,-0.36984,19.439,0.31614,-0.78837,-0.52776,516.07,-0.58097,0.27891,-0.76465,760.49
> view matrix models
> #1,0.72303,0.56221,-0.40143,31.263,0.28918,-0.77405,-0.56322,528.8,-0.62737,0.29114,-0.72225,758.09
> close #1
> open emdb:34638 format ccp4 fromDatabase emdb
Opened emdb 34638 as #1, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> close #1
> open emdb:34725 format ccp4 fromDatabase emdb
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #1 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> ui mousemode right "move picked models"
> view matrix models
> #2,0.16681,-0.88874,-0.42698,445.67,0.14475,0.45043,-0.881,153.31,0.97531,0.085159,0.20378,-225.87
> log metadata #2
Metadata for 8hfr #2
---
Title | NPC-trapped pre-60S particle
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Non-standard residue | MG — magnesium ion
Sources (natural) | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34725 — open map
Experimental method | Electron microscopy
Resolution | 2.64Å
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select /xI:107-211
524 atoms, 529 bonds, 1 pseudobond, 65 residues, 2 models selected
> volume #1 change image level -0.04277,0 level 0.2825,0.8 level 1.288,1
> volume #1 level 0.1227
> set bgColor gray
> set bgColor #80808000
> view matrix models #1,1,0,0,-9.2167,0,1,0,3.5023,0,0,1,34.289
> view matrix models #1,1,0,0,-39.047,0,1,0,51.27,0,0,1,115.24
> set silhouettes true
> view matrix models #1,1,0,0,-27.192,0,1,0,26.46,0,0,1,87.869
> select add #1
524 atoms, 529 bonds, 1 pseudobond, 65 residues, 5 models selected
> select add #1
524 atoms, 529 bonds, 1 pseudobond, 65 residues, 5 models selected
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 7 models
selected
> select add #1
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 7 models
selected
> select subtract #2
3 models selected
> ui mousemode right select
> select clear
> lighting default
> fitmap #2 inMap #1
Fit molecule 8hfr (#2) to map emdb 34725 (#1) using 152374 atoms
average map value = 0.0002081, steps = 2000
shifted from previous position = 1.65
rotated from previous position = 0.829 degrees
atoms outside contour = 152374, contour level = 0.12269
Position of 8hfr (#2) relative to emdb 34725 (#1) coordinates:
Matrix rotation and translation
0.16101218 -0.88612750 -0.43457237 474.59710764
0.15387957 0.45747211 -0.87580840 121.53838867
0.97488264 0.07414401 0.21001550 -311.16885662
Axis 0.47673216 -0.70733284 0.52192596
Axis point 472.60877052 0.00000000 203.94572937
Rotation angle (degrees) 94.91916023
Shift along axis -22.11949183
> ui mousemode right "move picked models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> select /UF:86@NZ
1 atom, 1 residue, 1 model selected
> view matrix models
> #2,0.16101,-0.88613,-0.43457,510.07,0.15388,0.45747,-0.87581,382.98,0.97488,0.074144,0.21002,-5.2998
> view matrix models
> #2,0.16101,-0.88613,-0.43457,517.38,0.15388,0.45747,-0.87581,349.87,0.97488,0.074144,0.21002,-5.5705
> view matrix models
> #2,0.16101,-0.88613,-0.43457,625.07,0.15388,0.45747,-0.87581,159.28,0.97488,0.074144,0.21002,-169.46
> view matrix models
> #2,0.16101,-0.88613,-0.43457,626.15,0.15388,0.45747,-0.87581,158.35,0.97488,0.074144,0.21002,-171.64
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> select add #1
3 models selected
> view matrix models #1,1,0,0,-10.664,0,1,0,34.89,0,0,1,42.427
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.15586,0.98116,0.1142,-80.24,-0.40189,0.1686,-0.90003,603.82,-0.90233,0.094382,0.42059,410.56
> view matrix models
> #1,0.26106,0.96047,0.096644,-97.83,-0.3756,0.19329,-0.9064,591.97,-0.88925,0.20033,0.41122,381.3
> view matrix models
> #1,0.3017,0.19181,0.93391,-126.92,0.86201,0.36362,-0.35315,71.466,-0.40733,0.91158,-0.05564,188.61
> view matrix models
> #1,0.098572,-0.59087,0.80072,171.52,0.92132,0.3583,0.15098,-77.511,-0.3761,0.72284,0.5797,61.004
> view matrix models
> #1,-0.38766,-0.76722,-0.51097,697.71,0.78171,-0.56738,0.25885,177.93,-0.48851,-0.29908,0.8197,299.66
> view matrix models
> #1,-0.5225,-0.85248,0.016657,615.13,0.76737,-0.46163,0.44502,103.71,-0.37168,0.24531,0.89536,103.09
> view matrix models
> #1,0.15248,-0.93038,-0.33338,551.08,0.71571,-0.12868,0.68644,-36.128,-0.68155,-0.34327,0.64627,408.84
> view matrix models
> #1,0.26576,-0.94918,0.16862,392,0.65901,0.30653,0.68684,-137.54,-0.70362,-0.071411,0.70698,325.81
> view matrix models
> #1,-0.104,-0.94606,-0.30685,615.97,0.26552,0.27091,-0.92526,406.8,0.95848,-0.1777,0.22302,44.197
> ui mousemode right "translate selected models"
> select /1e:2064@C4'
1 atom, 1 residue, 1 model selected
> view matrix models
> #2,0.16101,-0.88613,-0.43457,556.13,0.15388,0.45747,-0.87581,371.98,0.97488,0.074144,0.21002,-14.29
> view matrix models
> #2,0.16101,-0.88613,-0.43457,553.44,0.15388,0.45747,-0.87581,379.74,0.97488,0.074144,0.21002,-7.9904
> fitmap #2 inMap #1
Fit molecule 8hfr (#2) to map emdb 34725 (#1) using 152374 atoms
average map value = 0.3481, steps = 456
shifted from previous position = 19.9
rotated from previous position = 18.4 degrees
atoms outside contour = 45840, contour level = 0.12269
Position of 8hfr (#2) relative to emdb 34725 (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00001349 0.00001242 0.00516934
0.00001349 1.00000000 -0.00007504 0.01691477
-0.00001242 0.00007504 1.00000000 -0.02017291
Axis 0.97142648 0.16074122 0.17462203
Axis point 0.00000000 278.63777838 216.35340828
Rotation angle (degrees) 0.00442617
Shift along axis 0.00421791
> view matrix models
> #2,-0.10401,-0.94608,-0.30678,642.72,0.26554,0.27084,-0.92528,356.39,0.95847,-0.1777,0.22305,25.455
> undo
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> ui mousemode right zoom
> ui mousemode right zone
> zone /v9:409
> zone label false
> undo
[Repeated 9 time(s)]
> ui mousemode right zone
[Repeated 1 time(s)]
> zone clear
> zone /1e:1945
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 8 models
selected
> zone /1e:1919
> ui mousemode right select
> select clear
> select add #1
3 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.098572,-0.59087,0.80072,221.29,0.92132,0.3583,0.15098,20.131,-0.3761,0.72284,0.5797,49.264
> view matrix models
> #1,0.098572,-0.59087,0.80072,246.09,0.92132,0.3583,0.15098,60.522,-0.3761,0.72284,0.5797,61.325
> view matrix models
> #1,0.098572,-0.59087,0.80072,248.27,0.92132,0.3583,0.15098,57.343,-0.3761,0.72284,0.5797,76.91
> view matrix models
> #1,0.098572,-0.59087,0.80072,330.27,0.92132,0.3583,0.15098,199.54,-0.3761,0.72284,0.5797,98.017
> view matrix models
> #1,0.098572,-0.59087,0.80072,378.61,0.92132,0.3583,0.15098,314,-0.3761,0.72284,0.5797,44.203
> view matrix models
> #1,0.098572,-0.59087,0.80072,443.78,0.92132,0.3583,0.15098,424.66,-0.3761,0.72284,0.5797,66.055
> view matrix models
> #1,0.098572,-0.59087,0.80072,488.98,0.92132,0.3583,0.15098,478.56,-0.3761,0.72284,0.5797,130.61
> view matrix models
> #1,0.098572,-0.59087,0.80072,594.53,0.92132,0.3583,0.15098,696.81,-0.3761,0.72284,0.5797,81.586
> ui mousemode right select
> view sel
No displayed objects specified.
> select add #1
3 models selected
> hide #!2 models
> ui mousemode right zone
> zone label false
> zone clear
> close #1-2
> open 8HFR format mmcif fromDatabase pdb
8hfr title:
NPC-trapped pre-60S particle [more info...]
Chain information for 8hfr #1
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 8hfr #1
---
MG — magnesium ion
> close #1
> open emdb:34725 format ccp4 fromDatabase emdb
Opened emdb 34725 as #1, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #1 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> lighting full
> volume #1 level 0.9
> ui mousemode right "contour level"
> volume #1 level 0.1395
> volume #1 level 0.1231
> volume #1 encloseVolume 1e6 step 1
> volume #1 level 0.135
> volume #1 level 0.1263
> volume #1 level 0.1089
> volume #1 level 0.09394
> volume #1 level 0.8225
> volume #1 level 0.3978
> volume #1 level 0.1238
> volume #1 level 0.2646
> color tan
> volume #1 change image level -0.04277,0 level 0.2825,0.8 level 1.288,1
> volume #1 level 0.1975
> set silhouettes true
> set bgColor gray
> open 8HFR format mmcif fromDatabase pdb
8hfr title:
NPC-trapped pre-60S particle [more info...]
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 8hfr #2
---
MG — magnesium ion
> ui mousemode right select
> ui mousemode right rotate
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.1572
> volume #1 level 0.1807
> volume #1 level 0.17
> volume #1 level 0.192
> volume #1 level 0.185
> show #!2 models
> lighting default
> ui mousemode right "translate selected models"
> select /1e:2445@N3
1 atom, 1 residue, 1 model selected
> view matrix models #2,1,0,0,0.47427,0,1,0,-3.2112,0,0,1,-0.75048
> fitmap #2 inMap #1
Fit molecule 8hfr (#2) to map emdb 34725 (#1) using 152374 atoms
average map value = 0.1222, steps = 60
shifted from previous position = 1.23
rotated from previous position = 0.738 degrees
atoms outside contour = 117763, contour level = 0.185
Position of 8hfr (#2) relative to emdb 34725 (#1) coordinates:
Matrix rotation and translation
0.99993752 0.00167424 -0.01105247 3.60350322
-0.00174473 0.99997818 -0.00637173 -1.95980623
0.01104156 0.00639061 0.99991862 -4.99546376
Axis 0.49575565 -0.85824688 -0.13281050
Axis point 403.74453054 0.00000000 138.41810689
Rotation angle (degrees) 0.73750875
Shift along axis 4.13190472
> volume #1 transparency 0.5
> molmap #2 10
Opened 8hfr map 10 as #3, grid size 109,89,102, pixel 3.33, shown at level
0.0873, step 1, values float32
> volume #3 style mesh
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume subtract #1 #3 minRms true
Opened volume difference as #4, grid size 800,800,800, pixel 0.668, shown at
step 1, values float32
Minimum RMS scale factor for "8hfr map 10 #3" above level 0.087258 is 0.39047
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> volume #4 color pink
> transparency 0
> hide atoms
> show ribbons
> save C:/Users/CSLiao/Desktop/HW1.cxs
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show sel atoms
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> show sel atoms
> hide sel cartoons
> volume #2 transparency 0.5
No volumes specified
> transparency 50
> transparency 80
[Repeated 1 time(s)]
> transparency 100
> transparency 0
> transparency #2 90
> transparency #2 90 atoms
> transparency #2 60 atoms
> transparency #2 70 atoms
> hide sel atoms
> show sel cartoons
> transparency 0
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!3 models
> log metadata #2
Metadata for 8hfr #2
---
Title | NPC-trapped pre-60S particle
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Non-standard residue | MG — magnesium ion
Sources (natural) | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34725 — open map
Experimental method | Electron microscopy
Resolution | 2.64Å
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> open emdb:34641
Opened emdb 34641 as #5, grid size 320,320,320, pixel 0.668, shown at level
0.373, step 2, values float32
> close #5
> select /AN:101-477
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> view matrix models
> #2,0.99994,0.0016742,-0.011052,4.2478,-0.0017447,0.99998,-0.0063717,-1.9461,0.011042,0.0063906,0.99992,-5.842
> undo
> ui mousemode right select
> ui mousemode right rotate
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "contour level"
> volume #1 level 0.2336
> volume #3 level 0.102
> undo
> show #!2 models
> select add #1
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 5 models selected
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 7 models
selected
> select subtract #2
3 models selected
> volume #1 level 0.195
> select add #1
3 models selected
> ui mousemode right select
> select clear
> select add #1
3 models selected
> Hide Dust
Unknown command: Hide Dust
> surface dust #1 size 6.68
> save C:/Users/CSLiao/Desktop/HW1.cxs
——— End of log from Mon Nov 6 16:34:47 2023 ———
opened ChimeraX session
> volume #1 level 0.091
> volume #1 level 0.1078
> volume #1 level 0.102
> hide #!3 models
> show #!3 models
> hide #!2 models
> volume #3 level 0.1441
> volume #3 level 0.102
> show #!2 models
> hide #!1 models
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> select /AN:101-477
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN:101-477
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> view sel
> show #!1 models
> volume #1 level 0.104
> hide #!1 models
> select /CW:3-477
2120 atoms, 2116 bonds, 3 pseudobonds, 427 residues, 2 models selected
> view sel
> show #!1 models
> hide #!2 models
> lighting full
> lighting soft
> lighting simple
> lighting full
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> lighting shadows false
> graphics silhouettes false
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> view sel
> show #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> show sel atoms
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> select add #1
1786 atoms, 1808 bonds, 242 residues, 6 models selected
> color zone #1 near sel & #2 distance 4.01
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 9 models
selected
> hide #!3 models
> select subtract #2
5 models selected
> color #2 #d5a0f5ff
> color #2 #95f58eff
> volume #1 color #d2d2d0
> show #!2 models
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> show atoms
> color bychain
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 9 models
selected
> color sel bychain
> hide #!1 models
> view sel
> select /sm:24-173
1036 atoms, 1043 bonds, 150 residues, 1 model selected
> view sel
> color #2 #d8d8d8ff
> color #2 #d8d8d5ff
> color sel blue
> select /vV:153-405
1875 atoms, 1913 bonds, 1 pseudobond, 245 residues, 2 models selected
> color sel orange
> select /CW:3-477
2120 atoms, 2116 bonds, 3 pseudobonds, 427 residues, 2 models selected
> view sel
> color sel #ADFF2F
> color sel #7FFFD4
> save C:/Users/CSLiao/Desktop/HW1.cxs
> select /v9:157-465
748 atoms, 761 bonds, 1 pseudobond, 106 residues, 2 models selected
> color sel #800000
> color \Wg #006400
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /Wg #006400
> select /CW:3-477
2120 atoms, 2116 bonds, 3 pseudobonds, 427 residues, 2 models selected
> color /ox #191970
> color /xI #87CEFA
> show #!1 models
> color zone #1 near sel & #2 distance 4.01
> select add #1
2120 atoms, 2116 bonds, 3 pseudobonds, 427 residues, 7 models selected
> color zone #1 near sel & #2 distance 4.01
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 9 models
selected
> show #!2 models
> color zone #1 near sel & #2 distance 4.01
> hide #!2 models
> select subtract #2
5 models selected
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> view sel
> view
> ui mousemode right select
> select clear
> hide #!1 models
> show #!2 models
> color /pT #EE82EE
> color /qJ #BA55D3
> select /qJ:2-175
1022 atoms, 1033 bonds, 3 pseudobonds, 135 residues, 2 models selected
> color /pT #FF00FF
> color /rA #FF0000
> color /sm #00FFFF
> color /tB #00FF7F
> color /xd #000000
> save C:/Users/CSLiao/Desktop/HW1.cxs
> color /FR #FFFF00
> select /AN:101-477
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
Alignment identifier is 2/AN
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> blastprotein 2/AN:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1
Webservices job id: FYN08GVX8FJ475BM
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> select /AN
1843 atoms, 1841 bonds, 1 pseudobond, 371 residues, 2 models selected
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> select /yE:2-243
1786 atoms, 1808 bonds, 242 residues, 1 model selected
> color sel #7B68EE
> color \Zq #D3D3D3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color \Zq #D3D3D3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /Zq #D3D3D3
> select /As:1-217
1089 atoms, 1088 bonds, 217 residues, 1 model selected
> select /zp:2-106
668 atoms, 675 bonds, 1 pseudobond, 88 residues, 2 models selected
> color /AN #4B0082
> color /Bt #F5F5DC
> color /Bt #F0E68C
> save C:/Users/CSLiao/Desktop/HW1.cxs
> color /DK #FF00FF
> color /pT #FF69B4
> select /EX:101-477
1725 atoms, 1722 bonds, 2 pseudobonds, 347 residues, 2 models selected
> color /EX #006400
> color /EX #2F4F4F
> color /EX #006400
> color /EX #8FBC8F
> color /EX #008080
> select /FR:8-184
816 atoms, 814 bonds, 1 pseudobond, 165 residues, 2 models selected
> save C:/Users/CSLiao/Desktop/HW1.cxs
> open 8HFR
8hfr title:
NPC-trapped pre-60S particle [more info...]
Chain information for 8hfr #5
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 8hfr #5
---
MG — magnesium ion
> close #5
> open 8HBN
8hbn title:
Structure of the Mex67-Mtr2-1 heterodimer [more info...]
Chain information for 8hbn #5
---
Chain | Description | UniProt
A | mRNA export factor MEX67 | MEX67_YEAST 1-599
B | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
> open embd:34638
No such database 'embd'
> open emdb:34638
Opened emdb 34638 as #6, grid size 400,400,400, pixel 1.34, shown at level
0.0878, step 2, values float32
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> surface dust #6 size 13.4
> hide #!6 models
> log metadata #5
Metadata for 8hbn #5
---
Title | Structure of the Mex67-Mtr2-1 heterodimer
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34638 — open map
Experimental method | Electron microscopy
Resolution | 3.81Å
> log chains #5
Chain information for 8hbn #5
---
Chain | Description | UniProt
A | mRNA export factor MEX67 | MEX67_YEAST 1-599
B | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
> log metadata #5
Metadata for 8hbn #5
---
Title | Structure of the Mex67-Mtr2-1 heterodimer
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34638 — open map
Experimental method | Electron microscopy
Resolution | 3.81Å
> log chains #5
Chain information for 8hbn #5
---
Chain | Description | UniProt
A | mRNA export factor MEX67 | MEX67_YEAST 1-599
B | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
> select add #5
4189 atoms, 4275 bonds, 2 pseudobonds, 536 residues, 2 models selected
> log metadata #5
Metadata for 8hbn #5
---
Title | Structure of the Mex67-Mtr2-1 heterodimer
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34638 — open map
Experimental method | Electron microscopy
Resolution | 3.81Å
> log chains #5
Chain information for 8hbn #5
---
Chain | Description | UniProt
A | mRNA export factor MEX67 | MEX67_YEAST 1-599
B | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
> show #!6 models
> volume #6 level 0.1049
> open emdb: 4wwu
EMDB identifiers are at least 4 characters long
> open emdb:4wwu
Fetching url
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-4wwu/map/emd_4wwu.map.gz
failed:
<urlopen error ftp error: error_perm('550 Failed to change directory.')>
> open 4WWU
4wwu title:
Structure of Mex67:Mtr2 [more info...]
Chain information for 4wwu #7
---
Chain | Description | UniProt
A B D E G H J K | mRNA export factor MEX67 | MEX67_YEAST 1-487
C F I L | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
Non-standard residues in 4wwu #7
---
ZN — zinc ion
4wwu mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 5FL8
Summary of feedback from opening 5FL8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #8
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> close #8
> open 6n8k
6n8k title:
Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal
subunit [more info...]
Chain information for 6n8k #8
---
Chain | Description | UniProt
1 | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA |
2 | 5S rRNA |
3 | 5.8S rRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
o | 60S ribosomal protein L29 | RL29_YEAST 1-59
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
s | Ribosomal Protein uL1 |
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 6n8k #8
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> close #8
> open 3nc1
3nc1 title:
Crystal structure of the CRM1-RanGTP complex [more info...]
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
Non-standard residues in 3nc1 #8
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> close #7
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> select subtract #5
Nothing selected
> select add #1
3 models selected
> show #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 7 models
selected
> color zone #1 near sel & #2 distance 4.01
> hide #!2 models
> volume #1 level 0.108
> show #!8 models
> log metadata #8
Metadata for 3nc1 #8
---
Title | Crystal structure of the CRM1-RanGTP complex
Citation | Guttler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L.,
Monecke, T., Ficner, R., Sattler, M., Gorlich, D. (2010). NES consensus
redefined by structures of PKI-type and Rev-type nuclear export signals bound
to CRM1. Nat.Struct.Mol.Biol., 17, 1367-1376. PMID: 20972448. DOI:
10.1038/nsmb.1931
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Gene sources | Homo sapiens (human)
Mus musculus (mouse)
Experimental method | X-ray diffraction
Resolution | 3.350Å
> log chains #8
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
> select subtract #2
3 models selected
> select add #8
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 6 models selected
> select subtract #1
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 3 models selected
> hide #!1 models
> log metadata #8
Metadata for 3nc1 #8
---
Title | Crystal structure of the CRM1-RanGTP complex
Citation | Guttler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L.,
Monecke, T., Ficner, R., Sattler, M., Gorlich, D. (2010). NES consensus
redefined by structures of PKI-type and Rev-type nuclear export signals bound
to CRM1. Nat.Struct.Mol.Biol., 17, 1367-1376. PMID: 20972448. DOI:
10.1038/nsmb.1931
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Gene sources | Homo sapiens (human)
Mus musculus (mouse)
Experimental method | X-ray diffraction
Resolution | 3.350Å
> log chains #8
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
> show #!1 models
> log metadata #8
Metadata for 3nc1 #8
---
Title | Crystal structure of the CRM1-RanGTP complex
Citation | Guttler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L.,
Monecke, T., Ficner, R., Sattler, M., Gorlich, D. (2010). NES consensus
redefined by structures of PKI-type and Rev-type nuclear export signals bound
to CRM1. Nat.Struct.Mol.Biol., 17, 1367-1376. PMID: 20972448. DOI:
10.1038/nsmb.1931
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Gene sources | Homo sapiens (human)
Mus musculus (mouse)
Experimental method | X-ray diffraction
Resolution | 3.350Å
> log chains #8
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
> log metadata #8
Metadata for 3nc1 #8
---
Title | Crystal structure of the CRM1-RanGTP complex
Citation | Guttler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L.,
Monecke, T., Ficner, R., Sattler, M., Gorlich, D. (2010). NES consensus
redefined by structures of PKI-type and Rev-type nuclear export signals bound
to CRM1. Nat.Struct.Mol.Biol., 17, 1367-1376. PMID: 20972448. DOI:
10.1038/nsmb.1931
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Gene sources | Homo sapiens (human)
Mus musculus (mouse)
Experimental method | X-ray diffraction
Resolution | 3.350Å
> log chains #8
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
> volume #1 level 0.084
> volume #1 level 0.09709
> volume #1 level 0.09491
> volume #1 level 0.1
> hide #!1 models
> open emdb:34725
Opened emdb 34725 as #7, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #1 style mesh
> volume #1 style surface
> volume #1
> volume #7 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #7 style surface
> surface dust #7 size 6.68
> select add #1
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 6 models selected
> select subtract #8
3 models selected
> hide #!7 models
> hide #!8 models
> vop gaussian #1 sdev 2
Opened emdb 34725 gaussian as #9, grid size 800,800,800, pixel 0.668, shown at
step 1, values float32
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #9
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!7 models
> show #!7 models
> volume #1 level 0.117
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> volume #1 step 4
> hide #!7 models
> show #!7 models
> hide #!7 models
> volume #1 step 2
> volume #1 step 4
> volume #1 level 0.1
> volume #1 step 8
> volume #1 step 4
> volume #1 level 0.08
> volume #1 level 0.06249
> volume #1 level 0.06055
> volume #1 level 0.061
> volume #1 level 0.065
> volume #1 level 0.07
> volume #1 level 0.075
> volume #1 level 0.077
> volume #1 level 0.08
> volume #1 level 0.079
> volume #1 level 0.08
> volume #1 level 0.085
> volume #1 level 0.09
> volume #1 level 0.1
> volume #1 level 0.18
> volume #1 level 0.101
> volume #1 level 0.11
> volume #1 level 0.08
> volume #1 step 2
> volume #1 style mesh
> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 399,399,399 imageMode orthoplanes
> volume #1 style surface region 0,0,0,799,799,799 step 1
> surface dust #1 size 6.68
> volume #1 step 2
> open 5FL8
Summary of feedback from opening 5FL8 fetched from pdb
---
warning | PDB entry 5FL8 has been replaced by 5JCS
5fl8 title:
Cryo-em structure of the RIX1-REA1 pre-60S particle [more info...]
Chain information for 5fl8 #9
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> show #!2 models
> hide #!1 models
> select add #1
3 models selected
> select #9/s:1566@O
1 atom, 1 residue, 1 model selected
> select add #9
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> select clear
> sequence chain #9/y
Alignment identifier is 9/y
> show #!1 models
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> show #!2 models
> hide #!1 models
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> log metadata #9
Metadata for 5fl8 #9
---
Title | Cryo-em structure of the RIX1-REA1 pre-60S particle
Citation | Barrio-Garcia, C., Thoms, M., Flemming, D., KAter, L.,
Berninghausen, O., Bassler, J., Beckmann, R., Hurt, E. (2016). Architecture of
the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Nat.Struct.Mol.Biol., 23, 37-44. PMID: 26619264. DOI: 10.1038/nsmb.3132
Sources (natural) | Saccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (baker's yeast)
Saccharomyces cerevisiae (baker's yeast)
Experimental method | Electron microscopy
Resolution | 9.5Å
> log chains #9
Chain information for 5fl8 #9
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> select subtract #2
Nothing selected
> select add #9
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/u:1-380
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> select #9/z:1-121
2576 atoms, 2880 bonds, 61 pseudobonds, 121 residues, 2 models selected
> select #9/u
1519 atoms, 1518 bonds, 380 residues, 1 model selected
> view sel
> view all
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> show #!8 models
> hide #!9 models
> select add #9
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> select subtract #9
Nothing selected
> hide #!2 models
> log metadata #8
Metadata for 3nc1 #8
---
Title | Crystal structure of the CRM1-RanGTP complex
Citation | Guttler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L.,
Monecke, T., Ficner, R., Sattler, M., Gorlich, D. (2010). NES consensus
redefined by structures of PKI-type and Rev-type nuclear export signals bound
to CRM1. Nat.Struct.Mol.Biol., 17, 1367-1376. PMID: 20972448. DOI:
10.1038/nsmb.1931
Non-standard residues | GTP — guanosine-5'-triphosphate
MG — magnesium ion
Gene sources | Homo sapiens (human)
Mus musculus (mouse)
Experimental method | X-ray diffraction
Resolution | 3.350Å
> log chains #8
Chain information for 3nc1 #8
---
Chain | Description | UniProt
A | Exportin-1 | XPO1_MOUSE 1-1071
C | GTP-binding nuclear protein Ran | RAN_HUMAN 1-180
> select #8/C:8-180
1403 atoms, 1438 bonds, 173 residues, 1 model selected
> select add #8
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 3 models selected
> select subtract #8
Nothing selected
> select add #8
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 3 models selected
> view sel
> select subtract #8
Nothing selected
> select #8/A:10-1050
8313 atoms, 8481 bonds, 2 pseudobonds, 1026 residues, 2 models selected
> show #!5 models
> hide #!8 models
> select add #8
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 3 models selected
> select subtract #8
Nothing selected
> select add #5
4189 atoms, 4275 bonds, 2 pseudobonds, 536 residues, 2 models selected
> select #8/A:10-1050
8313 atoms, 8481 bonds, 2 pseudobonds, 1026 residues, 2 models selected
> view sel
[Repeated 1 time(s)]
> select add #8
9749 atoms, 9953 bonds, 6 pseudobonds, 1201 residues, 3 models selected
> log metadata #5
Metadata for 8hbn #5
---
Title | Structure of the Mex67-Mtr2-1 heterodimer
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Gene source | Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34638 — open map
Experimental method | Electron microscopy
Resolution | 3.81Å
> log chains #5
Chain information for 8hbn #5
---
Chain | Description | UniProt
A | mRNA export factor MEX67 | MEX67_YEAST 1-599
B | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
> select #5/B:8-184
1280 atoms, 1309 bonds, 1 pseudobond, 165 residues, 2 models selected
> view sel
> view all
> show #!2 models
> hide sel atoms
> select add #2
153654 atoms, 163599 bonds, 3372 pseudobonds, 14729 residues, 6 models
selected
> select add #5
156563 atoms, 166565 bonds, 3373 pseudobonds, 15100 residues, 6 models
selected
> hide sel atoms
> show sel atoms
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide sel atoms
> select clear
> hide #!2 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 step 1
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> select #5/B:8-184
1280 atoms, 1309 bonds, 1 pseudobond, 165 residues, 2 models selected
> hide #!6 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.11
> open emdb:35767
Opened emdb 35767 as #10, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #10 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> surface dust #6 size 13.4
> surface dust #10 size 6.68
> select add #10
1280 atoms, 1309 bonds, 1 pseudobond, 165 residues, 5 models selected
> surface dust #10 size 6.68
> hide #!2 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> close #7
> show #!5 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!10 models
> volume #10 step 1
> volume #10 step 16
> volume #10 step 2
> volume #10 level 0.1
> volume #10 change image level -0.009036,0 level 0.02513,0.8 level 0.04992,1
> volume #6 step 2
> volume #6 level 0.1
> show #!1 models
> volume #6 level 0.12
> volume #6 level 0.09
> volume #6 level 0.08
> volume #6 level 0.095
> volume #6 level 0.085
> volume #6 level 0.09
> volume #6 level 0.092
> volume #6 level 0.091
> volume #6 level 0.092
> close #4
> hide #!10 models
> hide #!6 models
> show #!8 models
> hide #!1 models
> hide #!8 models
> hide #!5 models
> show #!9 models
> select add #9
107088 atoms, 114856 bonds, 1115 pseudobonds, 13344 residues, 8 models
selected
> select clear
> select add #9
105808 atoms, 113547 bonds, 1114 pseudobonds, 13179 residues, 3 models
selected
> log metadata #9
Metadata for 5fl8 #9
---
Title | Cryo-em structure of the RIX1-REA1 pre-60S particle
Citation | Barrio-Garcia, C., Thoms, M., Flemming, D., KAter, L.,
Berninghausen, O., Bassler, J., Beckmann, R., Hurt, E. (2016). Architecture of
the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
Nat.Struct.Mol.Biol., 23, 37-44. PMID: 26619264. DOI: 10.1038/nsmb.3132
Sources (natural) | Saccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (baker's yeast)
Saccharomyces cerevisiae (baker's yeast)
Experimental method | Electron microscopy
Resolution | 9.5Å
> log chains #9
Chain information for 5fl8 #9
---
Chain | Description | UniProt
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | Rpl9ap | N1P1M8_YEASC 1-191
I | 60S ribosomal protein L1-B | RL1B_YEAST 1-217
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | 60S ribosomal protein L12-A | RL12A_YEAST 1-165
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
n | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
o | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome assembly protein 4 | NLE1_YEAST 1-515
r | Protein SDA1 | SDA1_YEAST 78-806
s | Midasin | MDN1_YEAST 1-4912
t | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
u | ARX1 |
x | 25S ribosomal RNA |
y | 5.8S ribosomal RNA |
z | 5S ribosomal RNA |
> select #9/H:1-191
763 atoms, 762 bonds, 191 residues, 1 model selected
> show #!2 models
> select add #2
153137 atoms, 163052 bonds, 3371 pseudobonds, 14755 residues, 5 models
selected
> hide sel atoms
> select add #9
258182 atoms, 275837 bonds, 4485 pseudobonds, 27743 residues, 7 models
selected
> select subtract #9
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select add #9
258182 atoms, 275837 bonds, 4485 pseudobonds, 27743 residues, 7 models
selected
> hide sel atoms
> show sel cartoons
> select #9/H:1-191
763 atoms, 762 bonds, 191 residues, 1 model selected
> log metadata #2
No models had metadata
> log chains #2
Chain information for 8hfr #2
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select #9/H:1-191
763 atoms, 762 bonds, 191 residues, 1 model selected
> select #2/tB:1-154
1246 atoms, 1273 bonds, 154 residues, 1 model selected
> ui tool show AlphaFold
> alphafold predict
> MSFFNRSNTTSALGTSTAMANEKDLANDIVINSPAEDSISDIAFSPQQDFMFSASSWDGKVRIWDVQNGVPQGRAQHESSSPVLCTRWSNDGTKVASGGCDNALKLYDIASGQTQQIGMHSAPIKVLRFVQCGPSNTECIVTGSWDKTIKYWDMRQPQPVSTVMMPERVYSMDNKQSLLVVATAERHIAIINLANPTTIFKATTSPLKWQTRCVACYNEADGYAIGSVEGRCSIRYIDDGMQKKSGFSFKCHRQTNPNRAPGSNGQSLVYPVNSIAFHPLYGTFVTAGGDGTFNFWDKNQRHRLKGYPTLQASIPVCSFNRNGSVFAYALSYDWHQGHMGNRPDYPNVIRLHATTDEEVKEKKKR
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
[Repeated 1 time(s)]
> hide #!9 models
> ui tool show AlphaFold
> open C:/Users/CSLiao/Downloads/ChimeraX/PDB/Gle2_alphafold_Uniport.pdb
Gle2_alphafold_Uniport.pdb title:
Alphafold monomer V2.0 prediction for nucleoporin GLE2 (P40066) [more info...]
Chain information for Gle2_alphafold_Uniport.pdb #4
---
Chain | Description | UniProt
A | nucleoporin GLE2 | GLE2_YEAST 1-365
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> view #4 clip false
> show #!2 models
> select subtract #2
Nothing selected
> ui mousemode right "translate selected models"
> select add #4
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> view matrix models #4,1,0,0,24.236,0,1,0,35.741,0,0,1,170.63
> view matrix models #4,1,0,0,66.456,0,1,0,94.453,0,0,1,254
> view matrix models #4,1,0,0,56.168,0,1,0,111.42,0,0,1,260.75
> view all
> view matrix models #4,1,0,0,41.642,0,1,0,112.74,0,0,1,192.51
> view matrix models #4,1,0,0,112.97,0,1,0,183.48,0,0,1,246.92
> hide #!2 models
> show #!6 models
> view matrix models #4,1,0,0,304.11,0,1,0,89.288,0,0,1,233.48
> view matrix models #4,1,0,0,459.11,0,1,0,277.53,0,0,1,212.89
> view matrix models #4,1,0,0,393.78,0,1,0,333.23,0,0,1,254.97
> view matrix models #4,1,0,0,391.37,0,1,0,334.84,0,0,1,257.07
> view matrix models #4,1,0,0,395.39,0,1,0,334.25,0,0,1,255.5
> view matrix models #4,1,0,0,387.96,0,1,0,328.84,0,0,1,255.76
> view matrix models #4,1,0,0,388.65,0,1,0,328.56,0,0,1,254.86
> show #!1 models
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.68373,0.7278,0.053136,392.16,-0.72475,0.66876,0.16581,329.86,0.085141,-0.15188,0.98473,254.06
> view matrix models
> #4,0.52778,-0.15332,0.83543,391.17,0.016802,0.98527,0.1702,328.81,-0.84922,-0.075791,0.52258,256.09
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.52778,-0.15332,0.83543,386.08,0.016802,0.98527,0.1702,326.41,-0.84922,-0.075791,0.52258,248.72
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.8664,-0.0074261,-0.4993,382.92,-0.48406,0.23307,-0.84342,323.24,0.12264,0.97243,0.19834,248.85
> view matrix models
> #4,0.88343,0.01457,-0.46833,383.01,-0.45566,0.25961,-0.85145,323.23,0.10918,0.9656,0.23598,248.94
> volume #6 level 0.08
> volume #6 level 0.02
> volume #6 level 0.04
> volume #6 step 8
> volume #6 level 0.06
> volume #6 step 4
> volume #6 level 0.04
> volume #6 level 0.08
> volume #6 step 2
> volume #6 level 0.092
> volume #6 level 0.07
> ui mousemode right "map eraser"
> volume erase #6 center 273.15,272.69,261.1 radius 78.458
Opened emdb 34638 copy as #11, grid size 400,400,400, pixel 1.34, shown at
step 1, values float32
> undo
> show #!10 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!6 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> hide #4 models
> show #4 models
> show #!11 models
> volume #11 step 2
> hide #!6 models
> close #11
> show #!6 models
> volume #6 level 0.06
> volume erase #6 center 381.76,325.55,247.13 radius 36.874 outside true
Opened emdb 34638 copy as #11, grid size 400,400,400, pixel 1.34, shown at
step 1, values float32
> rename #11 Gel2_from34638
> volume #11 level 0.065
> volume #11 level 0.07
> volume #11 step 2
> volume #11 level 0.06
> volume #11 level 0.04
> volume #11 level 0.05
> volume #11 level 0.06
> volume #11 level 0.07
> volume #11 level 0.075
> volume #11 level 0.08
> surface dust #11 size 13.4
> volume #11 level 0.04
> surface dust #11 size 13.4
> save C:/Users/CSLiao/Desktop/HW2.cxs
> hide #!11 models
> show #!6 models
> hide #4 models
> select subtract #4
Nothing selected
> volume #6 level 0.07
> volume erase #6 center 263.67,271.27,261.39 radius 82.565
Opened emdb 34638 copy as #12, grid size 400,400,400, pixel 1.34, shown at
step 1, values float32
> select add #12
2 models selected
> surface dust #12 size 13.4
> close #11
> undo
> open #11
'#11' has no suffix
> open model #11
'model' has no suffix
> volume #11
No volumes specified
> volume show
> volume hide
> show #!12 models
> select add #12
2 models selected
> volume erase #12 center 333.11,275.18,212.25 radius 98.33 outside true
> hide #!12 models
> show #!12 models
> close #12
> show #!6 models
> volume erase #6 center 331.32,275.62,225.66 radius 112.22 outside true
Opened emdb 34638 copy as #11, grid size 400,400,400, pixel 1.34, shown at
step 1, values float32
> select add #11
2 models selected
> surface dust #11 size 13.4
> volume erase #11 center 361.06,318.71,174.47 radius 29.926
> volume erase #11 center 374.37,293.73,306.38 radius 22.979
> volume erase #11 center 268.01,337.92,163.45 radius 22.979
> volume erase #11 center 272.15,275.85,259.6 radius 83.634
> volume #11 level 0.06
> volume erase #11 center 264.73,219.04,197.85 radius 47.027
> volume erase #11 center 284.92,226.36,192.34 radius 47.027
> volume erase #11 center 301.06,188.08,279.95 radius 47.027
> volume erase #11 center 322.83,230.58,343.18 radius 47.027
> volume erase #11 center 329.82,233.56,323.88 radius 47.027
> volume erase #11 center 314.7,290.88,310.6 radius 47.027
> volume erase #11 center 329.14,310.25,202.06 radius 24.85
> volume erase #11 center 323.28,275.38,192.2 radius 17.902
> volume erase #11 center 417.73,303.1,170.06 radius 17.902
> volume erase #11 center 415.55,343.47,208.33 radius 17.902
> volume erase #11 center 349.41,319.75,209.64 radius 17.902
> volume erase #11 center 347.92,240.6,176.77 radius 17.902
> rename #11 34638_clean
> save C:/Users/CSLiao/Desktop/HW2.cxs
> close #7
> volume #11 level 0.065
> volume #11 level 0.07
> volume #11 level 0.08
> volume #11 step 2
> volume #11 level 0.06
> close #7
> ui mousemode right rotate
> show #!1 models
> select subtract #11
Nothing selected
> select add #1
3 models selected
> volume #1 level 0.07
> hide #!11 models
> ui mousemode right "map eraser"
> select add #1
3 models selected
> select add #1
3 models selected
> ui mousemode right select
> select clear
> ui mousemode right "map eraser"
> volume erase #1 center 267.68,266.25,265.78 radius 169.14 outside true
Opened emdb 34725 copy as #12, grid size 800,800,800, pixel 0.668, shown at
step 1, values float32
> surface dust #12 size 6.68
> volume #12 step 2
> volume #12 step 1
> volume erase #12 center 257.37,99.689,266.32 radius 75.35
> volume #12 step 2
> volume #12 level 0.06
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume erase #12 center 376.45,112.24,255.45 radius 75.35
> volume erase #12 center 246.06,101.34,188.45 radius 75.35
> volume erase #12 center 271.93,89.672,200.58 radius 75.35
> volume erase #12 center 145.71,151.41,191.46 radius 75.35
> volume erase #12 center 432.31,308.18,385.62 radius 75.35
> volume copy #12 subregion 534,348,464,761,575,691
Opened emdb 34725 copy as #13, grid size 228,228,228, pixel 0.668, shown at
step 1, values float32
> show #!12 models
> close #13
> volume erase #12 center 389.87,116.02,239.54 radius 75.314
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> volume erase #12 center 200.03,105.86,299.54 radius 75.083
> volume erase #12 center 193.03,264.39,460.77 radius 75.083
> select add #12
2 models selected
> volume erase #12 center 303.01,340.21,480.49 radius 75.083
> volume erase #12 center 349.06,227.56,73.802 radius 75.083
> volume erase #12 center 325.6,355.46,77.408 radius 75.083
> volume erase #12 center 392.42,294.02,145.56 radius 28.858
> volume erase #12 center 450.04,273.35,232.23 radius 28.858
> volume erase #12 center 198.8,156.72,304.76 radius 28.858
> volume erase #12 center 317.11,138.3,216.45 radius 28.858
> volume sel style mesh
> volume sel style image
> volume sel style surface
> surface dust #12 size 6.68
> volume #12 step 2
> volume erase #12 center 144.89,307.75,171.65 radius 28.858
> volume erase #12 center 160.83,308.42,138.09 radius 28.858
> volume erase #12 center 224.3,172.95,143.57 radius 28.858
> volume erase #12 center 200.38,179.44,200.96 radius 28.858
> volume erase #12 center 370.16,368.72,300.14 radius 28.858
> volume #12 step 1
> volume #12 step 2
> close #7
> rename #12 34725_clean
> ui mousemode right "map eraser"
> volume erase #12 center 174.55,210.19,430.51 radius 62.525
> volume erase #12 center 95.843,320.42,255.55 radius 62.525
> volume erase #12 center 200.9,183.33,379.13 radius 39.813
> volume erase #12 center 143.46,155.91,252.76 radius 39.813
> volume erase #12 center 111.04,236.12,215.49 radius 39.813
> volume erase #12 center 99.174,175.04,310.28 radius 39.813
> ui mousemode right select
> select clear
> close #7
> show #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select add #12
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 7 models
selected
> color zone #12 near sel & #2 distance 4.01
> select clear
[Repeated 1 time(s)]
> volume #12 level 0.065
> hide #!2 models
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> ui mousemode right "translate selected models"
> select add #11
2 models selected
> ui mousemode right select
> select clear
> open emdb:34640
Opened emdb 34640 as #7, grid size 320,320,320, pixel 0.668, shown at level
0.105, step 2, values float32
> hide #!11 models
> hide #!12 models
> select clear
> close #13
> surface dust #7 size 6.68
> show #!11 models
> show #!12 models
> volume #7 level 0.07
> open 8HFR
8hfr title:
NPC-trapped pre-60S particle [more info...]
Chain information for 8hfr #13
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 8hfr #13
---
MG — magnesium ion
> rename #13 8HFR_copy
> save C:/Users/CSLiao/Desktop/HW3.cxs
> hide #!7 models
> show #!7 models
> hide #!11 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #13
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> log metadata #13
Metadata for 8HFR_copy #13
---
Title | NPC-trapped pre-60S particle
Citation | Li, Z., Chen, S., Zhao, L., Huang, G., Xu, H., Yang, X., Wang, P.,
Gao, N., Sui, S.F. (2023). Nuclear export of pre-60S particles through the
nuclear pore complex. Nature, 618, 411-418. PMID: 37258668. DOI:
10.1038/s41586-023-06128-y
Non-standard residue | MG — magnesium ion
Sources (natural) | Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
Saccharomyces cerevisiae S288C
CryoEM Map | EMDB 34725 — open map
Experimental method | Electron microscopy
Resolution | 2.64Å
> log chains #13
Chain information for 8HFR_copy #13
---
Chain | Description | UniProt
1e | 25S ribosomal RNA |
2f | 5S ribosomal RNA |
3n | 5.8S ribosomal RNA |
AN CW EX | mRNA export factor MEX67 | MEX67_YEAST 1-599
As | YEAST 60S ribosomal protein L1-A | RL1A_YEAST 1-217
B4 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
Bt DK FR | mRNA transport regulator MTR2 | MTR2_YEAST 1-184
CD | 60S ribosomal protein L3 | RL3_YEAST 1-387
DO | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
Ez | 60S ribosomal protein L5 | RL5_YEAST 1-297
F8 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
Gu | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
Hj | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
Ib | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
Jy | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
KM | YEAST 60S ribosomal protein L12-A | RL12A_YEAST 1-165
LL | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
MQ | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
No | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O6 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
Pv | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Qk | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
RP | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
SZ | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
Tl | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
UF | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V5 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
Wg | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
Xc | 60S ribosomal protein L25 | RL25_YEAST 0-141
YU | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Zq | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
aw | 60S ribosomal protein L28 | RL28_YEAST 1-149
b3 | 60S ribosomal protein L29 | RL29_YEAST 1-59
cC | 60S ribosomal protein L30 | RL30_YEAST 1-105
dG | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
eH | 60S ribosomal protein L32 | RL32_YEAST 1-130
f7 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g2 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h1 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
ia | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
jh | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
kr | 60S ribosomal protein L38 | RL38_YEAST 1-78
li | 60S ribosomal protein L39 | RL39_YEAST 1-51
mS | 60S ribosomal protein L42-A | RL44A_YEAST 1-106
nY | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
ox | Bud site selection protein 20 | BUD20_YEAST 1-166
pT | Probable metalloprotease ARX1 | ARX1_YEAST 1-593
qJ | Ribosome biogenesis protein ALB1 | ALB1_YEAST 1-175
rA | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
sm | Translation machinery-associated protein 16 | TMA16_YEAST 1-178
tB | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v9 | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
vV | 60S ribosomal export protein NMD3 | NMD3_YEAST 1-518
xI | Shuttling pre-60S factor ECM1 | ECM1_YEAST 1-212
xd | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
yE | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
zp | UPF0642 protein YBL028C | YBC8_YEAST 1-106
> select /CW:3-477
4240 atoms, 4232 bonds, 6 pseudobonds, 854 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99994,0.0016742,-0.011052,-51.213,-0.0017447,0.99998,-0.0063717,-120.03,0.011042,0.0063906,0.99992,-195.05,#13,1,0,0,-54.816,0,1,0,-118.07,0,0,1,-190.05
> view matrix models
> #2,0.99994,0.0016742,-0.011052,-51.103,-0.0017447,0.99998,-0.0063717,-119.6,0.011042,0.0063906,0.99992,-194.36,#13,1,0,0,-54.706,0,1,0,-117.64,0,0,1,-189.36
> view matrix models
> #2,0.99994,0.0016742,-0.011052,-51.664,-0.0017447,0.99998,-0.0063717,-120.98,0.011042,0.0063906,0.99992,-196.59,#13,1,0,0,-55.268,0,1,0,-119.02,0,0,1,-191.59
> mcopy #2 #13 settings a
Unknown command: mcopy #2 #13 settings a
> mcopy
Unknown command: mcopy
> hide #!13 models
> select add #13
154494 atoms, 164406 bonds, 3374 pseudobonds, 14991 residues, 6 models
selected
> show #!2 models
> show #!1 models
> select subtract #13
2120 atoms, 2116 bonds, 3 pseudobonds, 427 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> select subtract #2
Nothing selected
> show #!2 models
> ui mousemode right "translate selected models"
> select add #2
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 4 models
selected
> view matrix models
> #2,0.99994,0.0016742,-0.011052,16.179,-0.0017447,0.99998,-0.0063717,-55.481,0.011042,0.0063906,0.99992,5.7926
> view matrix models
> #2,0.99994,0.0016742,-0.011052,2.2291,-0.0017447,0.99998,-0.0063717,-30.388,0.011042,0.0063906,0.99992,-28.712
> view matrix models
> #2,0.99994,0.0016742,-0.011052,4.6527,-0.0017447,0.99998,-0.0063717,-39.458,0.011042,0.0063906,0.99992,-15.667
> hide #!1 models
> show #!12 models
> view matrix models
> #2,0.99994,0.0016742,-0.011052,1.4988,-0.0017447,0.99998,-0.0063717,-30.815,0.011042,0.0063906,0.99992,-27.912
> view matrix models
> #2,0.99994,0.0016742,-0.011052,-1.9476,-0.0017447,0.99998,-0.0063717,2.6943,0.011042,0.0063906,0.99992,-21.984
Must specify one map, got 0
> fitmap #2 inMap #12
Fit molecule 8hfr (#2) to map 34725_clean (#12) using 152374 atoms
average map value = 0.3481, steps = 200
shifted from previous position = 17.8
rotated from previous position = 0.735 degrees
atoms outside contour = 6848, contour level = 0.065
Position of 8hfr (#2) relative to 34725_clean (#12) coordinates:
Matrix rotation and translation
1.00000000 -0.00004450 -0.00003431 0.02625389
0.00004449 1.00000000 -0.00005259 0.00253493
0.00003431 0.00005259 1.00000000 -0.02664275
Axis 0.68338655 -0.44577705 0.57815711
Axis point 0.00000000 522.05873655 60.10610080
Rotation angle (degrees) 0.00440954
Shift along axis 0.00140785
> close #13
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> ui mousemode right "translate selected models"
> select add #7
152374 atoms, 162290 bonds, 3371 pseudobonds, 14564 residues, 6 models
selected
> select subtract #2
2 models selected
> view matrix models #7,1,0,0,2.4767,0,1,0,160.63,0,0,1,63.434
> view matrix models #7,1,0,0,54.903,0,1,0,131,0,0,1,204.43
> fitmap #7 inMap #12
Fit map emdb 34640 in map 34725_clean using 138716 points
correlation = 0.6102, correlation about mean = -0.08483, overlap = 1383
steps = 172, shift = 14.1, angle = 11 degrees
Position of emdb 34640 (#7) relative to 34725_clean (#12) coordinates:
Matrix rotation and translation
0.99093805 -0.07633137 0.11052288 57.55143545
0.09067801 0.98719832 -0.13121349 122.37423339
-0.09909229 0.14004643 0.98517395 191.28507196
Axis 0.71135210 0.54969489 0.43796543
Axis point 0.00000000 -744.20491115 200.95985377
Rotation angle (degrees) 10.99159639
Shift along axis 191.98407464
> volume #7 level 0.09
> hide #!12 models
> show #!12 models
> volume #7 level 0.1
> show #!11 models
> fitmap #11 inMap #12
Fit map 34638_clean in map 34725_clean using 17231 points
correlation = 0.6269, correlation about mean = 0.4554, overlap = 340.7
steps = 128, shift = 0.206, angle = 0.206 degrees
Position of 34638_clean (#11) relative to 34725_clean (#12) coordinates:
Matrix rotation and translation
0.99999416 0.00335197 0.00067186 -1.23425973
-0.00335272 0.99999376 0.00111027 0.94202505
-0.00066814 -0.00111252 0.99999916 0.61010349
Axis -0.30917054 0.18638285 -0.93256368
Axis point 280.94100476 369.79590441 0.00000000
Rotation angle (degrees) 0.20596511
Shift along axis -0.01178629
> show #4 models
Must specify one map, got 0
> fitmap #4 inMap #11
Fit molecule Gle2_alphafold_Uniport.pdb (#4) to map 34638_clean (#11) using
2847 atoms
average map value = 0.06946, steps = 84
shifted from previous position = 3.79
rotated from previous position = 9.46 degrees
atoms outside contour = 1180, contour level = 0.06
Position of Gle2_alphafold_Uniport.pdb (#4) relative to 34638_clean (#11)
coordinates:
Matrix rotation and translation
0.87372298 0.15086693 -0.46243628 386.16818312
-0.48546324 0.21073757 -0.84847811 321.46916285
-0.03055459 0.96583065 0.25736661 247.76765095
Axis 0.92070157 -0.21916564 -0.32291647
Axis point 0.00000000 4.05332719 428.08062063
Rotation angle (degrees) 80.15905919
Shift along axis 205.08240010
> select subtract #7
Nothing selected
> select add #4
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> show sel atoms
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!11 models
> hide #!12 models
> close #13
> select subtract #4
Nothing selected
> style #4#!2 sphere
Changed 155221 atom styles
> style #4#!2 ball
Changed 155221 atom styles
> style #4#!2 sphere
Changed 155221 atom styles
> color sel #20B2AA
> select add #4
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> color sel #20B2AA
> show #!12 models
> show #!11 models
> volume #11 level 0.05
> volume #11 level 0.04
> volume #11 step 4
> hide #4 models
> volume #11 step 2
> volume #11 step 1
> volume #11 step 2
> volume #11 level 0.01
> volume #11 level 0.05
> volume #11 level 0.06
> volume #11 level 0.07
> volume #11 level 0.05
> ui tool show "Color Zone"
> hide #!11 models
> show #!11 models
> color zone #11 near #4 distance 8.02
> color zone #11 near #2 distance 8.02
> color zone #11 near #2 distance 20.93
> color zone #11 near #2 distance 19.33
> volume splitbyzone #11
Opened 34638_clean 0 as #13.1, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 1 as #13.2, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 2 as #13.3, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 3 as #13.4, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 4 as #13.5, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 5 as #13.6, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 6 as #13.7, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 7 as #13.8, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 8 as #13.9, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 9 as #13.10, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 10 as #13.11, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 11 as #13.12, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 12 as #13.13, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 13 as #13.14, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 14 as #13.15, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 15 as #13.16, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 16 as #13.17, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 17 as #13.18, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 18 as #13.19, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 19 as #13.20, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
Opened 34638_clean 20 as #13.21, grid size 400,400,400, pixel 1.34, shown at
level 0.05, step 1, values float32
> hide #!13 models
> show #!11 models
> hide #!11 models
> show #!13 models
> surface dust #12 size 6.68
> surface dust #13.1 size 13.4
> surface dust #13.2 size 13.4
> surface dust #13.3 size 13.4
> surface dust #13.4 size 13.4
> surface dust #13.5 size 13.4
> surface dust #13.6 size 13.4
> surface dust #13.7 size 13.4
> surface dust #13.8 size 13.4
> surface dust #13.9 size 13.4
> surface dust #13.10 size 13.4
> surface dust #13.11 size 13.4
> surface dust #13.12 size 13.4
> surface dust #13.13 size 13.4
> surface dust #13.14 size 13.4
> surface dust #13.15 size 13.4
> surface dust #13.16 size 13.4
> surface dust #13.17 size 13.4
> surface dust #13.18 size 13.4
> surface dust #13.19 size 13.4
> surface dust #13.20 size 13.4
> surface dust #13.21 size 13.4
> select add #13.21
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select subtract #13.21
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.20
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select subtract #13.20
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.17
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select subtract #13.17
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.1
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select add #13.2
2847 atoms, 2917 bonds, 365 residues, 5 models selected
> select subtract #13.2
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> color zone #13.1 near #4 distance 8.02
> color zone #13.1 near #4 distance 8.84
> volume #13.1 level 0.06
> color zone #13.1 near #4 distance 13.14
> save C:/Users/CSLiao/Desktop/HW3.cxs
> select add #13.19
2847 atoms, 2917 bonds, 365 residues, 5 models selected
> select subtract #13.1
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> view sel
> select subtract #13.19
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.19
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select subtract #13.19
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.19
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select add #13.20
2847 atoms, 2917 bonds, 365 residues, 6 models selected
> select subtract #13.20
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> select subtract #13.19
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> select add #13.19
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> close #13.19
> select add #13.2
2847 atoms, 2917 bonds, 365 residues, 4 models selected
> close #13.2
> select add #13.3
2847 atoms, 2917 bonds, 365 residues, 3 models selected
> view sel
> select add #12
2847 atoms, 2917 bonds, 365 residues, 8 models selected
> select add #13
2847 atoms, 2917 bonds, 365 residues, 55 models selected
> select add #12
2847 atoms, 2917 bonds, 365 residues, 55 models selected
> select add #12
2847 atoms, 2917 bonds, 365 residues, 55 models selected
> ui mousemode right select
> select clear
> select add #13.1
2 models selected
> select subtract #13.1
Nothing selected
> select add #13.3
2 models selected
> select subtract #13.3
Nothing selected
> view all
> hide #!2 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> volume #12 level 0.07
> volume #12 step 4
> volume #12 step 2
> volume #12 level 0.08
> color zone #12 near #2 distance 4.01
> color zone #12 near #2 distance 5.04
> volume #12 level 0.085
> volume #12 level 0.09
> color zone #12 near #2 distance 7.69
> show #4 models
> select add #4
2847 atoms, 2917 bonds, 365 residues, 1 model selected
> color sel #008B8B
> color zone #13.1 near #4 distance 13.14
> show #!10 models
> hide #!10 models
> hide #!12 models
> hide #!13 models
> hide #4 models
> show #!10 models
> volume #10 color white
[Repeated 2 time(s)]
> volume #10 color #d9d9d9
> volume #6 level 0.04
> volume #6 level 0.07
> volume #10 level 0.05
> volume #10 level 0.01
> surface dust #10 size 6.68
> volume #10 level 0.04
> volume #10 level 0.08
> show #!11 models
> hide #!11 models
> show #!13 models
> show #!12 models
> hide #!10 models
> show #!10 models
> fitmap #10 to #12
Expected a keyword
> fitmap #10 inMap #12
Fit map emdb 35767 in map 34725_clean using 20329 points
correlation = 0.5646, correlation about mean = 0.05912, overlap = 455.7
steps = 432, shift = 49, angle = 34.8 degrees
Position of emdb 35767 (#10) relative to 34725_clean (#12) coordinates:
Matrix rotation and translation
0.97674764 0.10365133 0.18767114 -57.55352791
-0.18850150 0.83220716 0.52143880 4.24500088
-0.10213345 -0.54469041 0.83239481 265.21838269
Axis -0.93291698 0.25359367 -0.25564850
Axis point 0.00000000 441.53481390 127.60109569
Rotation angle (degrees) 34.84759875
Shift along axis -13.03351187
> hide #!10 models
> show #!10 models
> select add #10
2847 atoms, 2917 bonds, 365 residues, 4 models selected
> select add #10
2847 atoms, 2917 bonds, 365 residues, 4 models selected
> select add #10
2847 atoms, 2917 bonds, 365 residues, 4 models selected
> select add #10
2847 atoms, 2917 bonds, 365 residues, 4 models selected
> ui mousemode right "translate selected models"
> select subtract #4
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.97675,0.10365,0.18767,-66.92,-0.1885,0.83221,0.52144,-1.5124,-0.10213,-0.54469,0.83239,214.65
> hide #!12 models
> hide #!13 models
> show #!2 models
> view matrix models
> #10,0.97675,0.10365,0.18767,-68.037,-0.1885,0.83221,0.52144,11.522,-0.10213,-0.54469,0.83239,229.42
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.99062,0.04079,0.13045,-44.024,-0.093242,0.89953,0.42679,-20.852,-0.099938,-0.43494,0.89489,185.9
> view matrix models
> #10,0.98518,-0.073871,0.1548,-11.861,-0.00050346,0.90125,0.43329,-48.809,-0.17152,-0.42695,0.88786,204.99
> view matrix models
> #10,0.98189,-0.096262,0.16315,-5.5165,0.015932,0.90018,0.43523,-53.473,-0.18876,-0.42475,0.88541,209.63
> view matrix models
> #10,0.96623,-0.21458,0.14266,37.761,0.14667,0.91321,0.38018,-85.902,-0.21186,-0.34642,0.91384,188.15
> view matrix models
> #10,0.98376,-0.11068,0.14131,1.7467,0.044214,0.91243,0.40684,-60.713,-0.17396,-0.39399,0.9025,193.46
> undo
[Repeated 6 time(s)]
> show #!12 models
> undo
[Repeated 3 time(s)]
> view matrix models
> #10,0.87585,-0.15022,0.4586,4.5857,0.44326,-0.12533,-0.88759,335.41,0.19081,0.98068,-0.043181,-138.09
> view matrix models
> #10,-0.13269,-0.26263,-0.95573,549.62,-0.50796,-0.80998,0.2931,625.09,-0.8511,0.52437,-0.025936,293.06
> close #10
> open 35767
'35767' has no suffix
> open emdb:35767
Opened emdb 35767 as #10, grid size 800,800,800, pixel 0.668, shown at step 1,
values float32
> volume #10 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> surface dust #12 size 6.68
> surface dust #13.1 size 13.4
> surface dust #13.3 size 13.4
> surface dust #13.4 size 13.4
> surface dust #13.5 size 13.4
> surface dust #13.6 size 13.4
> surface dust #13.7 size 13.4
> surface dust #13.8 size 13.4
> surface dust #13.9 size 13.4
> surface dust #13.10 size 13.4
> surface dust #13.11 size 13.4
> surface dust #13.12 size 13.4
> surface dust #13.13 size 13.4
> surface dust #13.14 size 13.4
> surface dust #13.15 size 13.4
> surface dust #13.16 size 13.4
> surface dust #13.17 size 13.4
> surface dust #13.18 size 13.4
> surface dust #13.20 size 13.4
> surface dust #13.21 size 13.4
> surface dust #10 size 6.68
> volume #10 step 2
> volume #10 level 0.08
> volume #10 change image level -0.009036,0 level 0.02513,0.8 level 0.04992,1
> volume #10 step 1
> volume #10 level 0.07
> color zone #10 near #2 distance 4.01
> color zone #10 near #2 distance 5.56
> volume #10 color white
> volume #10 color #b1b1b1
> volume #10 color #bfbfbf
[Repeated 1 time(s)]
> volume #10 color #b6b9bf
> color zone #10 near #2 distance 5.56
> color zone #10 near #2 distance 8.74
> volume #10 level 0.1
> volume #10 step 2
> volume #10 level 0.15
> volume #10 level 0.1
> save C:/Users/CSLiao/Desktop/HW3.cxs
——— End of log from Tue Nov 7 17:16:20 2023 ———
opened ChimeraX session
> save C:/Users/CSLiao/Desktop/HW4.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 536.48
OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_TW.cp950
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: Acer
Model: Predator PO3-630
OS: Microsoft Windows 11 家用版 (Build 22621)
Memory: 34,205,884,416
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700F @ 2.50GHz
OSLanguage: zh-TW
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (3)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 2 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
comment:3 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
If I see this reported a few more times I will investigate whether it is an LZ4 memory leak.
Note:
See TracTickets
for help on using tickets.
The user simply opened a session and tried to save a session. So it is surprising that it failed with a memory error since they probably successfully saved this session on the same machine before. The computer has 32 GB memory and maximum process size of 128 GB, so it is hard to see how it got a memory error compressing the session.
The session saving is LZ4 compressing by opening the session file to write with lz4.frame.open(path, 'wb') and that causes the compression to happen as the data is written to the stream. This should not use up memory. Online I see a 2018 memory leak in Python LZ4 supposedly fixed and also a 2021 python lz4 test failure with memoryerror that was not solved and the test was simply removed.
My suspicion is that this is a Python LZ4 memory leak bug. We are using the most current Python PyPi LZ4 package version 4.3.2.
This session save memory error in LZ4 has been reported a number of times before.
We could attempt to make a test case and report a bug to the LZ4 maintainers.
The high memory use is probably originally from this command in the Log
creating many large volume models that is causing the memory error. For ever color being used on map #11 it is creating a copy of the map. Map #11 is 0.25 GB so if there were 100 colors it could be using 25 GB. It seems very unlikely that there are 100 colors in the color zone on that map.