Resource for Biocomputing, Visualization and Informatics
University of California, San Francisco
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Since 2009, there has been a rapid increase in number of available models of complex systems. These systems are often composed of dozens or even hundreds of proteins, frequently built using multiple experimental methods at varing resolutions and including flexible regions with poor structural detail, thus posing several challenges to the interactive visualization and analysis of their 3-D structures.
Source: Jasmine Young, RCSB
CRISPR: 5cd4. Two copies of the complex contained in the crystal asymmetric unit and defined in mmCIF assembly table. Each complex consists of 6 copies of CasC, 2 copies of CasB, 1 copy each of CasA, CasD, CasE (latter have identical sequences). 53,308 atoms.
Ribosome: 4v6w. 80 protein chains, 6 nucleic acid chains, 230,721 atoms.
Limitation: Because there are more than 62 chains and 100,000 atoms must use mmCIF data format.
Problem: Functional components not defined in mmCIF, so no way to visually explore things such as "large subunit" or the "peptide synthesis site" except by chain ID.
Nuclear pore complex: 736 copies of 20 proteins with 11 x-ray structure complexes (5HAX 5HAY 5HAZ 5HB0 5HB1 5HB2 5HB3 5HB4 5HB5 5HB6 5HB7 5HB8) fit into a cryoEM map (EMDB 3103), 8-fold symmetry, ~4,000,000 atoms.
Question: How would you find all contacts between 2 of the 8 "spoke" complexes, or between all channel and adaptor proteins?
(Length: ~15 minutes)
Source: Martin Beck lab, EMBL Heidelberg
Source: Andre Hoelz lab, Cal Tech
Source: Andrej Sali lab, UCSF
Integrative Models Task Force Workshop, EBI, October 2014