Computed structures of core eukaryotic protein complexes

被引：358

作者：

Humphreys, Ian R. ^{[1
,2
]}

Pei, Jimin ^{[3
,4
]}

Baek, Minkyung ^{[1
,2
]}

Krishnakumar, Aditya ^{[1
,2
]}

Anishchenko, Ivan ^{[1
,2
]}

Ovchinnikov, Sergey ^{[5
,6
]}

Zhang, Jing ^{[3
,4
]}

Ness, Travis J. ^{[7
]}

Banjade, Sudeep ^{[8
]}

Bagde, Saket R. ^{[8
]}

Stancheva, Viktoriya G. ^{[9
]}

Li, Xiao-Han ^{[9
]}

Liu, Kaixian ^{[10
]}

Zheng, Zhi ^{[10
,11
]}

Barrero, Daniel J. ^{[12
]}

Roy, Upasana ^{[13
]}

Kuper, Jochen ^{[14
]}

Fernandez, Israel S. ^{[15
]}

Szakal, Barnabas ^{[16
]}

Branzei, Dana ^{[16
,17
]}

Rizo, Josep ^{[4
,18
,19
]}

Kisker, Caroline ^{[14
]}

Greene, Eric C. ^{[13
]}

Biggins, Sue ^{[12
]}

Keeney, Scott ^{[10
,11
,20
]}

Miller, Elizabeth A. ^{[9
]}

Fromme, J. Christopher ^{[8
]}

Hendrickson, Tamara L. ^{[7
]}

Cong, Qian ^{[3
,4
]}

Baker, David ^{[1
,2
,21
]}

机构：

[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[2] Univ Washington, Inst Prot Design, Seattle, WA 98195 USA

[3] Univ Texas Southwestern Med Ctr Dallas, Eugene McDermott Ctr Human Growth & Dev, Dallas, TX 75390 USA

[4] Univ Texas Southwestern Med Ctr Dallas, Dept Biophys, Dallas, TX 75390 USA

[5] Harvard Univ, Fac Arts & Sci, Div Sci, Cambridge, MA 02138 USA

[6] Harvard Univ, John Harvard Distinguished Sci Fellowship Program, Cambridge, MA 02138 USA

[7] Wayne State Univ, Dept Chem, Detroit, MI 48202 USA

[8] Cornell Univ, Weill Inst Cell & Mol Biol, Dept Mol Biol & Genet, Ithaca, NY USA

[9] MRC Lab Mol Biol, Cambridge CB2 0QH, England

[10] Mem Sloan Kettering Canc Ctr, Mol Biol Program, 1275 York Ave, New York, NY 10021 USA

[11] Gerstner Sloan Kettering Grad Sch Biomed Sci, New York, NY USA

[12] Fred Hutchinson Canc Res Ctr, Howard Hughes Med Inst, Div Basic Sci, Seattle, WA 98104 USA

[13] Columbia Univ, Dept Biochem & Mol Biophys, New York, NY USA

[14] Univ Wurzburg, Rudolf Virchow Ctr Integrat & Translat Bioimaging, Wurzburg, Germany

[15] St Jude Childrens Res Hosp, Dept Struct Biol, 332 N Lauderdale St, Memphis, TN 38105 USA

[16] FIRC Inst Mol Oncol, IFOM, Via Adamello 16, I-20139 Milan, Italy

[17] Consiglio Nazl Ric IGM CNR, Ist Genet Mol, Via Abbiategrasso 207, I-27100 Pavia, Italy

[18] Univ Texas Southwestern Med Ctr Dallas, Dept Biochem, Dallas, TX USA

[19] Univ Texas Southwestern Med Ctr Dallas, Dept Pharmacol, Dallas, TX USA

[20] Mem Sloan Kettering Canc Ctr, Howard Hughes Med Inst, New York, NY 10021 USA

[21] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

来源：

SCIENCE | 2021年 / 374卷 / 6573期

基金：

英国医学研究理事会;

关键词：

DAM1 KINETOCHORE COMPLEX; DOUBLE-STRAND BREAKS; CRYO-EM STRUCTURE; GPI TRANSAMIDASE; CRYSTAL-STRUCTURE; GLYCOSYLPHOSPHATIDYLINOSITOL TRANSAMIDASE; INTERACTION NETWORKS; DNA-DAMAGE; SUBUNITS; PIG-T;

D O I：

10.1126/science.abm4805

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.

引用

页码：1340 / +

页数：69

共 112 条

[1]

Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites [J].

Agashe, Sumedha ;

Joseph, Chinnu Rose ;

Reyes, Teresa Anne Clarisse ;

Menolfi, Demis ;

Giannattasio, Michele ;

Waizenegger, Anja ;

Szakal, Barnabas ;

Branzei, Dana .

NATURE COMMUNICATIONS, 2021, 12 (01)

[2]

ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999

[3]

Antiviral protein Ski8 is a direct partner of Spo11 in meiotic DNA break formation, independent of its cytoplasmic role in RNA metabolism [J].

Arora, C ;

Kee, K ;

Maleki, S ;

Keeney, S .

MOLECULAR CELL, 2004, 13 (04) :549-559

[4]

The Dam1 kinetochore complex harnesses microtubule dynamics to produce force and movement [J].

Asbury, Charles L. ;

Gestaut, Daniel R. ;

Powers, Andrew F. ;

Franck, Andrew D. ;

Davis, Trisha N. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (26) :9873-9878

[5]

Accurate prediction of protein structures and interactions using a three-track neural network [J].

Baek, Minkyung ;

DiMaio, Frank ;

Anishchenko, Ivan ;

Dauparas, Justas ;

Ovchinnikov, Sergey ;

Lee, Gyu Rie ;

Wang, Jue ;

Cong, Qian ;

Kinch, Lisa N. ;

Schaeffer, R. Dustin ;

Millan, Claudia ;

Park, Hahnbeom ;

Adams, Carson ;

Glassman, Caleb R. ;

DeGiovanni, Andy ;

Pereira, Jose H. ;

Rodrigues, Andria V. ;

van Dijk, Alberdina A. ;

Ebrecht, Ana C. ;

Opperman, Diederik J. ;

Sagmeister, Theo ;

Buhlheller, Christoph ;

Pavkov-Keller, Tea ;

Rathinaswamy, Manoj K. ;

Dalwadi, Udit ;

Yip, Calvin K. ;

Burke, John E. ;

Garcia, K. Christopher ;

Grishin, Nick V. ;

Adams, Paul D. ;

Read, Randy J. ;

Baker, David .

SCIENCE, 2021, 373 (6557) :871-+

[6]

Banjade S, 2019, METHODS MOL BIOL, V1998, P105, DOI 10.1007/978-1-4939-9492-2_8

[7]

The yeast orthologue of GRASP65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffic [J].

Behnia, Rudy ;

Barr, Francis A. ;

Flanagan, John J. ;

Barlowe, Charles ;

Munro, Sean .

JOURNAL OF CELL BIOLOGY, 2007, 176 (03) :255-261

[8]

Structural and functional characterization of the Spo11 core complex [J].

Bouuaert, Corentin Claeys ;

Tischfield, Sam E. ;

Pu, Stephen ;

Mimitou, Eleni P. ;

Arias-Palomo, Ernesto ;

Berger, James M. ;

Keeney, Scott .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2021, 28 (01) :92-102

[9]

A SNARE required for retrograde transport to the endoplasmic reticulum [J].

Burri, L ;

Varlamov, O ;

Doege, CA ;

Hofmann, K ;

Beilharz, T ;

Rothman, JE ;

Söllner, TH ;

Lithgow, T .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (17) :9873-9877

[10]

CATCHR, HOPS and CORVET tethering complexes share a similar architecture [J].

Chou, Hui-Ting ;

Dukovski, Danijela ;

Chambers, Melissa G. ;

Reinisch, Karin M. ;

Walz, Thomas .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2016, 23 (08) :761-+

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