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Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Bai R, Wan R et al. Science. 2021 Jan 8;371(6525):eabe8863.

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Guo H, Courbon GM et al. Nature. 2021 Jan 7;589(7840):143-147.

Structure of the class D GPCR Ste2 dimer coupled to two G proteins. Velazhahan V, Ma N et al. Nature. 2021 Jan 7;589(7840):148-153.

Causes and consequences of RNA polymerase II stalling during transcript elongation. Noe Gonzalez M, Blears D, Svejstrup JQ. Nat Rev Mol Cell Biol. 2021 Jan;22(1):3-21.

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Saltzberg DJ, Viswanath S et al. Protein Sci. 2021 Jan;30(1):250-261.

See also: RCSB PDB Images
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News

December 11, 2020

The RBVI wishes you a safe and happy holiday season! See our 2020 card and the gallery of previous cards back to 1985.

November 4, 2020

New paper online: UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, et al. Protein Sci. 2020, in press.

September 23, 2020

Mac users: ChimeraX v1.1 does not work on MacOS 11.0 (Big Sur), but this problem has been fixed in v1.1.1 and the daily build.

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UCSF ChimeraX

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

5v8m chain network screenshot

Interactive Chain Network

Chain-chain interfaces can be identified by buried surface areas and displayed as a network diagram with the interfaces command or the Molecule Display icon . In the diagram, nodes (circles) represent chains, larger for greater surface areas, and edges (lines) between nodes represent chain-chain interfaces (default ≥ 300 Å2 buried area). Dotted lines represent interfaces smaller than half the size of the largest in the structure. Diagram context menus enable a variety of actions, such as “exploding” the structure by moving chains apart, hiding all but the chains in contact with a given chain, and showing a more detailed plot of the residues forming a given interface.

The structure is an HIV envelope glycoprotein trimer bound by three copies of a broadly neutralizing antibody (PDB 5v8m), with chain information shown in the Log. Glycosylations (not displayed) were included in the surface area calculations. For setup, see the command file trimer-network.cxc.

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Example Image

The Human Ribosome

The architecture of the human ribosome has been determined at near-atomic resolution by electron microscopy (Anger et al., Nature 497:80 (2013)). The structure, comprising 82 proteins and five RNA molecules, is shown with shadows cast from all directions to accentuate depth. In the background are schematic representations of contacts between the component molecules.

See the image setup script card.cxc using the 'Tis the Season color palette (credit to MrsP). See also the RBVI holiday card gallery.

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