UCSF ChimeraX: Meeting modern challenges in visualization and analysis

Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C.; Pettersen, Eric F.; Couch, Gregory S.; Morris, John H.; Ferrin, Thomas E.

doi:10.1002/pro.3235

Cited by 3,985 publications

(3,222 citation statements)

References 49 publications

(46 reference statements)

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“…First, individual subunits and tRNAs were fitted as rigid bodies into the densities. Cryo-EM structures and models were displayed with UCSF Chimera (Pettersen et al, 2004) ChimeraX (Goddard et al, 2018) or PYMOL (Version 2.0 Schrödinger, LLC). The protein components in the disome interface required only minor adjustments.…”

Section: Model Buildingmentioning

confidence: 99%

Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways

et al. 2019

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Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC+) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGDRQC−) can occur in a Not4‐dependent manner.

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Section: Model Buildingmentioning

confidence: 99%

Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways

et al. 2019

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“…First, individual subunits and tRNAs were fitted as rigid bodies into the densities. Cryo-EM structures and models were displayed with UCSF Chimera (Pettersen et al, 2004) and ChimeraX (Goddard et al, 2018). Cryo-EM structures and models were displayed with UCSF Chimera (Pettersen et al, 2004) and ChimeraX (Goddard et al, 2018).…”

Section: Model Buildingmentioning

confidence: 99%

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

et al. 2019

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Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall-and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.

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“…The ChimeraX visualization program 14 displays molecular structures and 3D microscopy data and has approximately one hundred diverse analysis capabilities. In 2014 we began adding the capability to display and manipulate this data using high-end VR headsets (https://www.rbvi.ucsf.edu/Outreach/Dissemination/OculusRift.pdf).…”

Section: Resultsmentioning

confidence: 99%

Molecular Visualization on the Holodeck

Goddard

Brilliant

Skillman³

et al. 2018

Journal of Molecular Biology

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Can virtual reality be useful for visualizing and analyzing molecular structures and 3-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching school children about biomolecules that are the machinery of life. What are the advantages and disadvantages of virtual reality for these applications? Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. We describe unique aspects of VR user interfaces, and the software and hardware advances needed for this technology to come into routine use for scientific data analysis.

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UCSF ChimeraX: Meeting modern challenges in visualization and analysis

Cited by 3,985 publications

References 49 publications

Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways

Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

Molecular Visualization on the Holodeck

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