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PRISM‐EM : template interface‐based modelling of multi‐protein complexes guided by cryo‐electron microscopy density maps
Author(s) -
Kuzu Guray,
Keskin Ozlem,
Nussinov Ruth,
Gursoy Attila
Publication year - 2016
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798316013541
Subject(s) - prism , envelope (radar) , trimer , ternary operation , cryo electron microscopy , crystallography , electron microscope , triangular prism , microscopy , benchmark (surveying) , biological system , materials science , computer science , chemistry , physics , optics , biology , nuclear magnetic resonance , telecommunications , radar , dimer , programming language , geodesy , geography
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three‐dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM‐EM , is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM‐EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM‐EM was then used to predict the structure of the ternary complex of the HIV‐1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.