HIV-1 envelope and MPER antibody structures in lipid assemblies. Rantalainen K, Berndsen ZT et al. Cell Rep. 2020 Apr 28;31(4):107583.
Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Kang G, Taguchi AT et al. Science. 2020 Apr 24;368(6489):424-427.
The Ccr4-Not complex monitors the translating ribosome for codon optimality. Buschauer R, Matsuo Y et al. Science. 2020 Apr 17;368(6488). pii: eaay6912.
Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Walls AC, Park YJ et al. Cell. 2020 Apr 16;181(2):281-292.e6.
Cryo-EM structure of the RNA-rich plant mitochondrial ribosome. Waltz F, Soufari H et al. Nat Plants. 2020 Apr;6(4):377-383.See also: RCSB PDB Images
May 8, 2020
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May 6, 2020
April 3, 2020Previous news...
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 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.
The matchmaker command is convenient for superimposing related structures without having to worry about numbering or missing residues. It superimposes proteins (and nucleic acids) by creating a pairwise sequence alignment, then matching the sequence-aligned residues in 3D. Secondary structure helps guide the sequence alignment for better performance on more distantly related proteins with harder-to-align sequences. By default, the fit is iterated to exclude structurally dissimilar regions and superimpose the most similar parts more closely.
The resulting sequence alignments can be displayed, as in this example of three pectate lyases: PDB 1jta, 1bn8, and 2pec. In the sequence alignments, residues used in the final fit iteration are enclosed in light orange boxes. RMSD values and other fit statistics are reported in the Log. For setup other than structure orientation, see the command file peclyases.cxc.More features...
The photosynthetic reaction center from a purple sulfur bacterium is shown as a cartoon with “tube” helices and membrane boundaries from the OPM database (Orientations of Proteins in Membranes, entry 1eys). Blue and red balls represent the cytoplasmic and periplasmic sides of the bacterial inner membrane, respectively. The title and other text labels were added with the 2dlabels command and repositioned interactively with the move label mouse mode . ChimeraX session file: prc.cxs
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