Cryo-EM map interpretation and protein model-building using iterative map segmentation

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

doi:10.1002/pro.3740

Title: Cryo-EM map interpretation and protein model-building using iterative map segmentation

Journal Article · 24 October 2019 · Protein Science

DOI: https://doi.org/10.1002/pro.3740 · OSTI ID:1571696

^[1]; Adams, Paul D. ^[2]; Afonine, Pavel V. ^[3]; Sobolev, Oleg V. ^[3]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a C_α model. The C_α model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); Phenix Industrial Consortium; National Institutes of Health (NIH); USDOE Office of Science (SC)

Grant/Contract Number:: 89233218CNA000001; AC02-05CH11231; AC52-06NA25396; GM063210; AC02‐05CH11231; AC5206NA25396

OSTI ID:: 1571696

Alternate ID(s):: OSTI ID: 1571697; OSTI ID: 1615287; OSTI ID: 1630869; OSTI ID: 1869629

Report Number(s):: LA-UR-19-31493; LA-UR-22-22634

Journal Information:: Protein Science, Vol. 29, Issue 1; ISSN 0961-8368

Publisher:: The Protein SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 20 works

Citation information provided by
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