Cryo‐EM map interpretation and protein model‐building using iterative map segmentation
Abstract
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 Cα model. The Cα 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.
- Authors:
-
[1];
- Los Alamos National Laboratory Los Alamos New Mexico, New Mexico Consortium Los Alamos New Mexico
- Molecular Biophysics &, Integrated Bioimaging DivisionLawrence Berkeley National Laboratory Berkeley California, Department of BioengineeringUniversity of California Berkeley Berkeley California
- Molecular Biophysics &, Integrated Bioimaging DivisionLawrence Berkeley National Laboratory Berkeley California
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC); Phenix Industrial Consortium; National Institutes of Health (NIH)
- OSTI Identifier:
- 1571696
- Alternate Identifier(s):
- OSTI ID: 1571697; OSTI ID: 1615287; OSTI ID: 1630869
- Report Number(s):
- LA-UR-19-31493
Journal ID: ISSN 0961-8368
- Grant/Contract Number:
- AC02‐05CH11231; AC02-05CH11231; 89233218CNA000001; AC52-06NA25396; GM063210
- Resource Type:
- Published Article
- Journal Name:
- Protein Science
- Additional Journal Information:
- Journal Name: Protein Science Journal Volume: 29 Journal Issue: 1; Journal ID: ISSN 0961-8368
- Publisher:
- The Protein Society
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological Science; cryo-electron microscopy; map interpretation; map segmentation; model-building
Citation Formats
Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Cryo‐EM map interpretation and protein model‐building using iterative map segmentation. United Kingdom: N. p., 2019.
Web. doi:10.1002/pro.3740.
Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., & Sobolev, Oleg V. Cryo‐EM map interpretation and protein model‐building using iterative map segmentation. United Kingdom. doi:10.1002/pro.3740.
Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Thu .
"Cryo‐EM map interpretation and protein model‐building using iterative map segmentation". United Kingdom. doi:10.1002/pro.3740.
@article{osti_1571696,
title = {Cryo‐EM map interpretation and protein model‐building using iterative map segmentation},
author = {Terwilliger, Thomas C. and Adams, Paul D. and Afonine, Pavel V. and Sobolev, Oleg V.},
abstractNote = {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 Cα model. The Cα 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.},
doi = {10.1002/pro.3740},
journal = {Protein Science},
number = 1,
volume = 29,
place = {United Kingdom},
year = {2019},
month = {10}
}
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DOI: 10.1002/pro.3740
DOI: 10.1002/pro.3740
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