Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

被引：9

作者：

Terwilliger, Thomas C. ^{[1
,2
]}

Sobolev, Oleg, V ^{[3
]}

Afonine, Pavel, V ^{[3
]}

Adams, Paul D. ^{[3
,4
]}

Ho, Chi-Min ^{[5
,6
,7
,8
]}

Li, Xiaorun ^{[7
,9
]}

Zhou, Z. Hong ^{[5
,6
,7
]}

机构：

[1] New Mexico Consortium, Los Alamos, NM 87544 USA

[2] Los Alamos Natl Lab, Biosci Div, Mail Stop M888, Los Alamos, NM 87545 USA

[3] Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA

[4] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA USA

[5] Univ Calif Los Angeles, Mol Biol Inst, Los Angeles, CA 90095 USA

[6] Univ Calif Los Angeles, Dept Microbiol Immunol & Mol Genet, Los Angeles, CA 90095 USA

[7] Univ Calif Los Angeles, Calif NanoSyst Inst, Los Angeles, CA 90095 USA

[8] Columbia Univ, Vagelos Coll Phys & Surg, Dept Microbiol & Immunol, New York, NY USA

[9] Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2021年 / 77卷

基金：

美国国家卫生研究院;

关键词：

cryo-EM; structural biology; model building; map interpretation;

D O I：

10.1107/S2059798321001765

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 angstrom, as well as using 91 deposited maps with resolutions between 2 and 4.5 angstrom. The approach is found to be highly effective for maps obtained at resolutions of 3.5 angstrom and better, and to have some utility at resolutions as low as 4 angstrom.

引用

页码：457 / 462

页数：6

共 22 条

[1] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[2] The translation elongation cycle-capturing multiple states by cryo-electron microscopy [J].

Frank, Joachim .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2017, 372 (1716)

[3] Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu [J].

Ho, Chi-Min ;

Li, Xiaorun ;

Lai, Mason ;

Terwilliger, Thomas C. ;

Beck, Josh R. ;

Wohlschlegel, James ;

Goldberg, Daniel E. ;

Fitzpatrick, Anthony W. P. ;

Zhou, Z. Hong .

NATURE METHODS, 2020, 17 (01) :79-+

[4]

Javed A., 2019, 722611 BIORXIV

[5] Capturing protein communities by structural proteomics in a thermophilic eukaryote [J].

Kastritis, Panagiotis L. ;

O'Reilly, Francis J. ;

Bock, Thomas ;

Li, Yuanyue ;

Rogon, Matt Z. ;

Buczak, Katarzyna ;

Romanov, Natalie ;

Betts, Matthew J. ;

Bui, Khanh Huy ;

Hagen, Wim J. ;

Hennrich, Marco L. ;

Mackmull, Marie-Therese ;

Rappsilber, Juri ;

Russell, Robert B. ;

Bork, Peer ;

Beck, Martin ;

Gavin, Anne-Claude .

MOLECULAR SYSTEMS BIOLOGY, 2017, 13 (07) :1-13

[6] NON-DARWINIAN EVOLUTION [J].

KING, JL ;

JUKES, TH .

SCIENCE, 1969, 164 (3881) :788-+

[7] Integrative biology of native cell extracts: a new era for structural characterization of life processes [J].

Kyrilis, Fotis L. ;

Meister, Annette ;

Kastritis, Panagiotis L. .

BIOLOGICAL CHEMISTRY, 2019, 400 (07) :831-846

[8] EMDataBank.org: unified data resource for CryoEM [J].

Lawson, Catherine L. ;

Baker, Matthew L. ;

Best, Christoph ;

Bi, Chunxiao ;

Dougherty, Matthew ;

Feng, Powei ;

van Ginkel, Glen ;

Devkota, Batsal ;

Lagerstedt, Ingvar ;

Ludtke, Steven J. ;

Newman, Richard H. ;

Oldfield, Tom J. ;

Rees, Ian ;

Sahni, Gaurav ;

Sala, Raul ;

Velankar, Sameer ;

Warren, Joe ;

Westbrook, John D. ;

Henrick, Kim ;

Kleywegt, Gerard J. ;

Berman, Helen M. ;

Chiu, Wah .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D456-D464

[9] Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix [J].

Liebschner, Dorothee ;

Afonine, Pavel V. ;

Baker, Matthew L. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Croll, Tristan I. ;

Hintze, Bradley ;

Hung, Li-Wei ;

Jain, Swati ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert D. ;

Poon, Billy K. ;

Prisant, Michael G. ;

Read, Randy J. ;

Richardson, Jane S. ;

Richardson, David C. ;

Sammito, Massimo D. ;

Sobolev, Oleg V. ;

Stockwell, Duncan H. ;

Terwilliger, Thomas C. ;

Urzhumtsev, Alexandre G. ;

Videau, Lizbeth L. ;

Williams, Christopher J. ;

Adams, Paul D. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2019, 75 :861-877

[10] Challenges and opportunities in cryo-EM single-particle analysis [J].

Lyumkis, Dmitry .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2019, 294 (13) :5181-5197

← 1 2 3 →