Changes between Version 4 and Version 5 of HIVspikes

Timestamp:

Sep 25, 2009, 12:34:53 PM (17 years ago)

Author:

goddard

Comment:

--

HIVspikes

@@ -36 +36 @@
 conformation can be found from the EM tomography data, averaging and fitting.
 
+||[[Image(emdb_5019.gif)]]||[[Image(emdb_5020.gif)]]||
+||Unliganded HIV-1 BaL spike. Subramaniam lab.[[BR]]EMDB 5019, PDB 3dnn||CD4 and 17b-bound HIV-1 BaL spike.[[BR]]EMDB 5020, PDB 3dno||
+
+[[Image(emdb_1246.gif)]]
+
+SIV envelope spike. Roux lab.[[BR]]
+EMDB 1246, PDB 2bf1 (gp120), PDB 1tji (gp41), PDB 1tzg (gp41) 
+
+There is some conflicting data about what trimeric spikes look like,
+having a single stalk in the viral envelope, or 3 legs (seen in SIV).
+
+I have SIV spike tomography from Ping Zhu in Kenneth Roux's lab and Florida State University.
+
+||[[Image(ping-zhu_with-molecule.jpg)]]||[[Image(dr-roux_at-electron-mircoscope_6-8-2005.jpg)]]||
+
+Structures aren't available for the two new bNAbs.  (None are reported in the article.)
+So we'll be looking at gp120 structures with other anti-bodies bound and CD4 bound.
+
+Start with PDB 1GC1 from 1998 having gp120 (red), a bound FAB (fragment antibody) (blue) and CD4 (yellow).
+
+[[Image(1gc1.png)]]
+
+Blast against the gp120 sequence (Model Panel / blast protein...).  The current Chimera interface
+doesn't let you specify a chain.  We don't want CD4 and other FAB structures, so first delete all
+but gp120 (chain G) then do the blast.
+
+[[Image(1gc1G_blast.png)]]
+