Isotropic reconstruction for electron tomography with deep learning.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
29 10 2022
29 10 2022
Historique:
received:
14
09
2021
accepted:
05
10
2022
pubmed:
31
10
2022
medline:
2
11
2022
entrez:
30
10
2022
Statut:
epublish
Résumé
Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ. However, anisotropic resolution arising from the intrinsic "missing-wedge" problem has presented major challenges in visualization and interpretation of tomograms. Here, we have developed IsoNet, a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. Therefore, by overcoming two fundamental limitations of cryoET, IsoNet enables functional interpretation of cellular tomograms without sub-tomogram averaging. Its application to high-resolution cellular tomograms should also help identify differently oriented complexes of the same kind for sub-tomogram averaging.
Identifiants
pubmed: 36309499
doi: 10.1038/s41467-022-33957-8
pii: 10.1038/s41467-022-33957-8
pmc: PMC9617606
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6482Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM071940
Pays : United States
Organisme : NIH HHS
ID : S10 OD018111
Pays : United States
Organisme : NCRR NIH HHS
ID : S10 RR023057
Pays : United States
Informations de copyright
© 2022. The Author(s).
Références
Sci Rep. 2020 Jun 26;10(1):10489
pubmed: 32591588
Curr Biol. 2008 Mar 25;18(6):R259-61
pubmed: 18364232
Elife. 2019 Nov 11;8:
pubmed: 31710293
Nat Methods. 2021 Nov;18(11):1386-1394
pubmed: 34675434
Nat Methods. 2021 Feb;18(2):203-211
pubmed: 33288961
J Struct Biol. 2019 May 1;206(2):183-192
pubmed: 30872095
Annu Rev Biochem. 2005;74:833-65
pubmed: 15952904
J Cell Biol. 2010 Jan 11;188(1):145-56
pubmed: 20065095
J Struct Biol. 1996 Jan-Feb;116(1):71-6
pubmed: 8742726
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774
Nature. 2020 Dec;588(7838):498-502
pubmed: 32805734
J Neurosci. 2018 Feb 7;38(6):1493-1510
pubmed: 29311144
Nat Methods. 2019 Nov;16(11):1153-1160
pubmed: 31591578
Nat Methods. 2012 Sep;9(9):853-4
pubmed: 22842542
J Struct Biol. 2017 Sep;199(3):187-195
pubmed: 28743638
Nat Methods. 2017 Aug;14(8):793-796
pubmed: 28671674
J Cell Sci. 1999 Nov;112 ( Pt 21):3769-77
pubmed: 10523512
Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11105-8
pubmed: 21690369
J Struct Biol. 2016 Jul;195(1):100-12
pubmed: 27079261
J Struct Biol. 2012 May;178(2):189-98
pubmed: 22285651
Curr Opin Struct Biol. 2019 Feb;54:129-138
pubmed: 30925443
J Struct Biol. 2015 Nov;192(2):216-21
pubmed: 26278980
Science. 2016 Jul 29;353(6298):506-8
pubmed: 27417497
Cell Discov. 2021 Jul 13;7(1):51
pubmed: 34257277
Sci Adv. 2020 Jul 22;6(30):eaba8397
pubmed: 32743076
PLoS One. 2012;7(1):e25700
pubmed: 22235240
Curr Opin Struct Biol. 2019 Feb;54:152-160
pubmed: 30904821
IEEE Trans Image Process. 2020 Sep 30;PP:
pubmed: 32997627
Annu Rev Biochem. 2018 Jun 20;87:871-896
pubmed: 29661000
Science. 2020 Oct 9;370(6513):203-208
pubmed: 32817270
Nat Neurosci. 2020 Dec;23(12):1589-1596
pubmed: 33139942
Nat Commun. 2020 Oct 15;11(1):5208
pubmed: 33060581
Nature. 2020 Nov;587(7832):157-161
pubmed: 33087927
J Struct Biol. 2013 Feb;181(2):169-78
pubmed: 23178680
Nat Struct Mol Biol. 2019 Oct;26(10):890-898
pubmed: 31582853
Ann Transl Med. 2020 Jun;8(11):713
pubmed: 32617333
Nat Protoc. 2016 Nov;11(11):2054-65
pubmed: 27685097
Elife. 2018 May 29;7:
pubmed: 29809143
Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):
pubmed: 33397805
Chem Rev. 2011 Dec 14;111(12):7710-48
pubmed: 21919528
Cell. 2020 Oct 29;183(3):730-738.e13
pubmed: 32979942
Structure. 2019 Apr 2;27(4):679-691.e14
pubmed: 30744995
Mach Vis Appl. 2018 Nov;29(8):1227-1236
pubmed: 31511756
Nat Methods. 2016 May;13(5):387-8
pubmed: 27067018
J Struct Biol. 2005 Oct;152(1):36-51
pubmed: 16182563
Acta Crystallogr D Struct Biol. 2019 May 1;75(Pt 5):467-474
pubmed: 31063149
Methods Cell Biol. 2019;152:277-289
pubmed: 31326025
Trends Biochem Sci. 2022 Feb;47(2):173-186
pubmed: 34511334
J Struct Biol. 2021 Jun;213(2):107742
pubmed: 33971285
Methods Enzymol. 2016;579:329-67
pubmed: 27572733
Nat Commun. 2016 Oct 18;7:13223
pubmed: 27752045
Commun Biol. 2019 Jun 19;2:218
pubmed: 31240256
Nat Methods. 2017 Apr;14(4):331-332
pubmed: 28250466
J Cell Sci. 2010 Feb 15;123(Pt 4):505-9
pubmed: 20144998
Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14266-71
pubmed: 26578771
Nat Methods. 2019 Nov;16(11):1146-1152
pubmed: 31591575
Neuron. 2000 Mar;25(3):649-62
pubmed: 10774732
Bioinformatics. 2017 Jul 15;33(14):i13-i22
pubmed: 28881965
Nat Methods. 2017 Oct;14(10):983-985
pubmed: 28846087
Nat Methods. 2009 Nov;6(11):817-23
pubmed: 19838170
J Struct Biol. 1997 Dec;120(3):343-52
pubmed: 9441937