Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.
Fanconi anemia core complex
cryoEM
deep learning
distance predictions
Journal
IUCrJ
ISSN: 2052-2525
Titre abrégé: IUCrJ
Pays: England
ID NLM: 101623101
Informations de publication
Date de publication:
01 Sep 2020
01 Sep 2020
Historique:
received:
07
04
2020
accepted:
07
07
2020
entrez:
17
9
2020
pubmed:
18
9
2020
medline:
18
9
2020
Statut:
epublish
Résumé
Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4-8 Å), with visible secondary-structure elements but poorly resolved loops, making model building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This paper describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using
Identifiants
pubmed: 32939280
doi: 10.1107/S2052252520009306
pii: eh5009
pmc: PMC7467173
doi:
Types de publication
Journal Article
Langues
eng
Pagination
881-892Subventions
Organisme : Medical Research Council
ID : MC_U105192715
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : R01 GM123089
Pays : United States
Informations de copyright
© Daniel P. Farrell et al. 2020.
Références
Nat Methods. 2014 Jan;11(1):63-5
pubmed: 24213166
Elife. 2016 Sep 26;5:
pubmed: 27669148
Curr Opin Virol. 2011 Aug;1(2):110-7
pubmed: 21845206
Nat Methods. 2018 Nov;15(11):905-908
pubmed: 30377346
Biophys J. 2016 Feb 23;110(4):766-75
pubmed: 26772592
Nature. 2017 Aug 17;548(7667):352-355
pubmed: 28682307
Nature. 2020 Jan;577(7792):706-710
pubmed: 31942072
J Virol. 2015 Jan 15;89(2):1182-94
pubmed: 25378500
Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3054-3059
pubmed: 29507254
Nature. 2013 Mar 28;495(7442):520-3
pubmed: 23515159
Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):17003-17010
pubmed: 32632011
Structure. 2015 May 5;23(5):949-960
pubmed: 25914056
Protein Sci. 2014 Jun;23(6):747-59
pubmed: 24639379
Nat Commun. 2018 Apr 24;9(1):1618
pubmed: 29691408
J Biol Chem. 2019 Mar 29;294(13):5181-5197
pubmed: 30804214
Protein Sci. 2018 Jan;27(1):245-258
pubmed: 28960548
Annu Rev Biochem. 2009;78:723-42
pubmed: 19489732
BMC Bioinformatics. 2019 Sep 14;20(1):473
pubmed: 31521110
Elife. 2018 Feb 09;7:
pubmed: 29424687
J Mol Biol. 2009 Sep 11;392(1):181-90
pubmed: 19596339
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Proteins. 2019 Dec;87(12):1149-1164
pubmed: 31365149
Nat Commun. 2018 Dec 19;9(1):5385
pubmed: 30568167
Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1496-1503
pubmed: 31896580
Proteins. 2014 Feb;82 Suppl 2:208-18
pubmed: 23900763
Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1540-7
pubmed: 22645369
Science. 2017 Mar 17;355(6330):1181-1184
pubmed: 28302852
Protein Sci. 2007 May;16(5):947-55
pubmed: 17456745
Bioinformatics. 2020 Jan 1;36(1):41-48
pubmed: 31173061
J Struct Biol. 2016 Dec;196(3):289-298
pubmed: 27436409
J Mol Biol. 2010 Apr 2;397(3):852-63
pubmed: 20036256
Cell Rep. 2014 Jul 10;8(1):20-30
pubmed: 24953649
Bioinformatics. 1998;14(9):755-63
pubmed: 9918945
Elife. 2014 May 01;3:e02030
pubmed: 24842992
Nature. 2019 Nov;575(7781):234-237
pubmed: 31666700
Proteins. 2019 Dec;87(12):1092-1099
pubmed: 31298436
Structure. 2019 Sep 3;27(9):1384-1394.e4
pubmed: 31303482
Elife. 2020 Jan 17;9:
pubmed: 31951201
BMC Struct Biol. 2018 Sep 15;18(1):12
pubmed: 30219048
Structure. 2019 Jan 2;27(1):175-188.e6
pubmed: 30393052
Nature. 2018 Mar 22;555(7697):475-482
pubmed: 29539637
Structure. 2013 Oct 8;21(10):1735-42
pubmed: 24035711