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UCSF ChimeraX Citations

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Selected Citations

In situ architecture of the ER-mitochondria encounter structure. Wozny MR, Di Luca A et al. Nature. 2023 Jun 1;618(7963):188–192.

Structural basis of catalytic activation in human splicing. Schmitzová J, Cretu C et al. Nature. 2023 May 25;617(7962):842-850.

Structural atlas of a human gut crassvirus. Bayfield OW, Shkoporov AN et al. Nature. 2023 May 11;617(7960):409-416.

mRNA decoding in human is kinetically and structurally distinct from bacteria. Holm M, Natchiar SK et al. Nature. 2023 May 4;617(7959):200–207.

Cryptochrome-Timeless structure reveals circadian clock timing mechanisms. Lin C, Feng S et al. Nature. 2023 May 4;617(7959):194–199.

De novo design of protein interactions with learned surface fingerprints. Gainza P, Wehrle S et al. Nature. 2023 May 4;617(7959):176-184.

mRNA recognition and packaging by the human transcription-export complex. Pacheco-Fiallos B, Vorländer MK et al. Nature. 2023 Apr 27;616(7958):828–835.

Structural study of the Cobetia marina bacteriophage 1 (Carin-1) by cryo-EM. d'Acapito A, Roret T et al. J Virol. 2023 Apr 27;97(4):e0024823.

Mirusviruses link herpesviruses to giant viruses. Gaïa M, Meng L et al. Nature. 2023 Apr 27;616(7958):783–789.

Top-down design of protein architectures with reinforcement learning. Lutz ID, Wang S et al. Science. 2023 Apr 21;380(6642):266-273.

Structural mechanisms for regulation of GSDMB pore-forming activity. Zhong X, Zeng H et al. Nature. 2023 Apr 20;616(7957):598–605.

Sensory specializations drive octopus and squid behaviour. Kang G, Allard CAH et al. Nature. 2023 Apr 13;616(7956):378-383.

Cryo-EM structure of the transposon-associated TnpB enzyme. Nakagawa R, Hirano H et al. Nature. 2023 Apr 13;616(7956):390-397.

Protein complexes in cells by AI-assisted structural proteomics. O'Reilly FJ, Graziadei A et al. Mol Syst Biol. 2023 Apr 12;19(4):e11544.

In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex. You X, Zhang X et al. Nature. 2023 Apr 6;616(7955):199–206.

Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase. Ge W, Yu C et al. Nature. 2023 Apr 6;616(7955):176–182.

Likelihood-based docking of models into cryo-EM maps. Millán C, McCoy AJ et al. Acta Crystallogr D Struct Biol. 2023 Apr 1;79(Pt 4):281-289.

Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex. Mühleip A, Flygaard RK et al. Nature. 2023 Mar 30;615(7954):934–938.

Structural basis of odorant recognition by a human odorant receptor. Billesbølle CB, de March CA et al. Nature. 2023 Mar 23;615(7953):742–749.

Structures of BIRC6-client complexes provide a mechanism of Smac-mediated release of caspases. Hunkeler M, Jin CY, Fischer ES. Science. 2023 Mar 17;379(6637):1105-1111.

Blebs promote cell survival by assembling oncogenic signalling hubs. Weems AD, Welf ES et al. Nature. 2023 Mar 16;615(7952):517-525.

Architecture of chloroplast TOC-TIC translocon supercomplex. Liu H, Li A et al. Nature. 2023 Mar 9;615(7951):349–357.

Coordination of bacterial cell wall and outer membrane biosynthesis. Hummels KR, Berry SP et al. Nature. 2023 Mar 9;615(7951):300–304.

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Kim SK, Dickinson MS et al. Nat Struct Mol Biol. 2023 Mar;30(3):296-308.

Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter. Fan M, Zhang J et al. Nature. 2023 Feb 23;614(7949):788–793.

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Mensah MA, Niskanen H et al. Nature. 2023 Feb 16;614(7948):564–571.

Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Cui Z, Napolitano G et al. Nature. 2023 Feb 16;614(7948):572–579.

Visualization of translation and protein biogenesis at the ER membrane. Gemmer M, Chaillet ML et al. Nature. 2023 Feb 2;614(7946):160–167.

Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN. Kinman LF, Powell BM et al. Nat Protoc. 2023 Feb;18(2):319-339.

Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Bridges HR, Blaza JN et al. Science. 2023 Jan 27;379(6630):351-357.

Undecaprenyl phosphate translocases confer conditional microbial fitness. Sit B, Srisuknimit V et al. Nature. 2023 Jan 26;613(7945):721-728.

Structures of the holo CRISPR RNA-guided transposon integration complex. Park JU, Tsai AW et al. Nature. 2023 Jan 26;613(7945):775-782.

RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2. Bravo JPK, Hallmark T et al. Nature. 2023 Jan 19;613(7944):582–587.

A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Otsuka S, Tempkin JOB et al. Nature. 2023 Jan 19;613(7944):575–581.

Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Rodrigues-Oliveira T, Wollweber F et al. Nature. 2023 Jan 12;613(7943):332–339.

Integrated intracellular organization and its variations in human iPS cells. Viana MP, Chen J et al. Nature. 2023 Jan 12;613(7943):345–354.

Structure of monkeypox virus DNA polymerase holoenzyme. Peng Q, Xie Y et al. Science. 2023 Jan 6;379(6627):100-105.

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Lugmayr W, Kotov V et al. Nat Protoc. 2023 Jan;18(1):239-264.

Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Xiong Q, Cao L et al. Nature. 2022 Dec 22;612(7941):748–757.

Multifunctional protein A is the only viral protein required for nodavirus RNA replication crown formation. den Boon JA, Zhan H et al. Viruses. 2022 Dec 3;14(12):2711.

ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Ermel UH, Arghittu SM, Frangakis AS. Protein Sci. 2022 Dec;31(12):e4472.

Starting a new chapter on class Ia ribonucleotide reductases. Levitz TS, Drennan CL. Curr Opin Struct Biol. 2022 Dec;77:102489.

Structure determination of inactive-state GPCRs with a universal nanobody. Robertson MJ, Papasergi-Scott MM et al. Nat Struct Mol Biol. 2022 Dec;29(12):1188-1195.

Structural principles of B cell antigen receptor assembly. Dong Y, Pi X et al. Nature. 2022 Dec 1;612(7938):156–161.

Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. Liu S, Xia X et al. Cell Discov. 2022 Nov 22;8(1):126.

Structure of the human heparan sulfate polymerase complex EXT1-EXT2. Leisico F, Omeiri J et al. Nat Commun. 2022 Nov 19;13(1):7110.

Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Jespersen N, Ehrenbolger K et al. Nat Commun. 2022 Nov 15;13(1):6962.

Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel. Mount J, Maksaev G et al. Nat Commun. 2022 Nov 12;13(1):6904.

Cryo-EM structure of the SEA complex. Tafur L, Hinterndorfer K et al. Nature. 2022 Nov 10;611(7935):399–404.

Structural basis of actin filament assembly and aging. Oosterheert W, Klink BU et al. Nature. 2022 Nov 10;611(7935):374–379.

Molecular glue CELMoD compounds are regulators of cereblon conformation. Watson ER, Novick S et al. Science. 2022 Nov 4;378(6619):549-553.

Mechanism of an intramembrane chaperone for multipass membrane proteins. Smalinskaitė L, Kim MK et al. Nature. 2022 Nov 3;611(7934):161-166.

Dual targeting factors are required for LXG toxin export by the bacterial type VIIb secretion system. Klein TA, Grebenc DW et al. mBio. 2022 Oct 26;13(5):e0213722.

MTCH2 is a mitochondrial outer membrane protein insertase. Guna A, Stevens TA et al. Science. 2022 Oct 21;378(6617):317-322.

Structure of the hepatitis C virus E1E2 glycoprotein complex. Torrents de la Peña A, Sliepen K et al. Science. 2022 Oct 21;378(6617):263-269.

A wheat resistosome defines common principles of immune receptor channels. Förderer A, Li E et al. Nature. 2022 Oct 20;610(7932):532-539.

ScanNet: A web server for structure-based prediction of protein binding sites with geometric deep learning. Tubiana J, Schneidman-Duhovny D, Wolfson HJ. J Mol Biol. 2022 Oct 15;434(19):167758.

Structural basis for directional chitin biosynthesis. Chen W, Cao P et al. Nature. 2022 Oct 13;610(7931):402-408.

Hallucinating symmetric protein assemblies. Wicky BIM, Milles LF et al. Science. 2022 Oct 7;378(6615):56-61.

Visualizing translation dynamics at atomic detail inside a bacterial cell. Xue L, Lenz S et al. Nature. 2022 Oct 6;610(7930):205-211.

Columnar structure of human telomeric chromatin. Soman A, Wong SY et al. Nature. 2022 Sep 29;609(7929):1048-1055.

Activation of the human insulin receptor by non-insulin-related peptides. Kirk NS, Chen Q et al. Nat Commun. 2022 Sep 28;13(1):5695.

Autoantibody mimicry of hormone action at the thyrotropin receptor. Faust B, Billesbølle CB et al. Nature. 2022 Sep 22;609(7928):846-853.

Mechanistic understanding of human SLFN11. Metzner FJ, Wenzl SJ et al. Nat Commun. 2022 Sep 17;13(1):5464.

Organizing structural principles of the IL-17 ligand-receptor axis. Wilson SC, Caveney NA et al. Nature. 2022 Sep 15;609(7927):622-629.

Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration. Wald J, Fahrenkamp D et al. Nature. 2022 Sep 15;609(7927):630-639.

Membranes under the magnetic lens: A dive into the diverse world of membrane protein structures using cryo-EM. Piper SJ, Johnson RM et al. Chem Rev. 2022 Sep 14;122(17):13989-14017.

R-loop formation and conformational activation mechanisms of Cas9. Pacesa M, Loeff L et al. Nature. 2022 Sep 1;609(7925):191-196.

Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Arvindekar S, Jackman MJ et al. Protein Sci. 2022 Sep;31(9):e4387.

Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA. Kuhle B, Hirschi M et al. Nat Commun. 2022 Aug 30;13(1):5100.

Structural plasticity enables evolution and innovation of RuBisCO assemblies. Liu AK, Pereira JH et al. Sci Adv. 2022 Aug 26;8(34):eadc9440.

Cryo-EM structure of an active bacterial TIR-STING filament complex. Morehouse BR, Yip MCJ et al. Nature. 2022 Aug 25;608(7924):803-807.

Structures of the human CST-Polα-primase complex bound to telomere templates. He Q, Lin X et al. Nature. 2022 Aug 25;608(7924):826-832.

Structures of the nitrogenase complex prepared under catalytic turnover conditions. Rutledge HL, Cook BD et al. Science. 2022 Aug 19;377(6608):865-869.

Cryo-EM structure of the human IgM B cell receptor. Su Q, Chen M et al. Science. 2022 Aug 19;377(6608):875-880.

ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Low JS, Jerak J et al. Science. 2022 Aug 12;377(6607):735-742.

Cryo-EM structures of human hepatitis B and woodchuck hepatitis virus small spherical subviral particles. Liu H, Hong X et al. Sci Adv. 2022 Aug 5;8(31):eabo4184.

Akkermansia muciniphila phospholipid induces homeostatic immune responses. Bae M, Cassilly CD et al. Nature. 2022 Aug 4;608(7921):168-173.

2.2 Å cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center. Chen EH, Kao HW et al. J Am Chem Soc. 2022 Aug 3;144(30):13888-13894.

Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels. Teng B, Kaplan JP et al. eLife. 2022 Aug 3;11:e77946.

Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography. Chmielewski D, Schmid MF et al. Nat Microbiol. 2022 Aug;7(8):1270-1279.

In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains. van den Hoek H, Klena N et al. Science. 2022 Jul 29;377(6605):543-548.

The cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Bücker R, Seuring C et al. Nat Commun. 2022 Jul 27;13(1):4356.

Structure of the nutrient-sensing hub GATOR2. Valenstein ML, Rogala KB et al. Nature. 2022 Jul 21;607(7919):610–616.

Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Suzuki S, Iida M et al. Commun Biol. 2022 Jul 15;5(1):707.

AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps. Hryc CF, Baker ML. iScience. 2022 Jul 15;25(7):104496.

Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD. Su S, Wang J et al. Nature. 2022 Jul 14;607(7918):399-406.

Mpe1 senses the binding of pre-mRNA and controls 3' end processing by CPF. Rodríguez-Molina JB, O'Reilly FJ et al. Mol Cell. 2022 Jul 7;82(13):2490-2504.e12.

eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Lapointe CP, Grosely R et al. Nature. 2022 Jul 7;607(7917):185-190.

Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators. Selvakumar P, Fernández-Mariño AI et al. Nat Commun. 2022 Jul 4;13(1):3854.

Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains. Case JB, Mackin S et al. Nat Commun. 2022 Jul 2;13(1):3824.

Mechanism of replication origin melting nucleated by CMG helicase assembly. Lewis JS, Gross MH et al. Nature. 2022 Jun 30;606(7916):1007-1014.

Structural insights into the HBV receptor and bile acid transporter NTCP. Park JH, Iwamoto M et al. Nature. 2022 Jun 30;606(7916):1027-1031.

Filamentation modulates allosteric regulation of PRPS. Hu HH, Lu GM et al. eLife. 2022 Jun 23;11:e79552.

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Fraser A, Sokolova ML et al. Nat Commun. 2022 Jun 20;13(1):3526.

Structural basis of nucleosome retention during transcription elongation. Filipovski M, Soffers JHM et al. Science. 2022 Jun 17;376(6599):1313-1316.

Structure of the rabies virus glycoprotein trimer bound to a prefusion-specific neutralizing antibody. Callaway HM, Zyla D et al. Sci Adv. 2022 Jun 17;8(24):eabp9151.

Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Itoh Y, Khawaja A et al. Nature. 2022 Jun 16;606(7914):603-608.

Structural remodeling of ribosome associated Hsp40-Hsp70 chaperones during co-translational folding. Chen Y, Tsai B et al. Nat Commun. 2022 Jun 14;13(1):3410.

Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold. Fontana P, Dong Y et al. Science. 2022 Jun 10;376(6598):eabm9326.

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