Atomic structures determined from digitally defined nanocrystalline regions.

atomic resolution electron crystallography electron-diffraction tomography nanocrystallography structure determination tilt series

Journal

IUCrJ
ISSN: 2052-2525
Titre abrégé: IUCrJ
Pays: England
ID NLM: 101623101

Informations de publication

Date de publication:
01 May 2020
Historique:
received: 19 11 2019
accepted: 22 03 2020
entrez: 21 5 2020
pubmed: 21 5 2020
medline: 21 5 2020
Statut: epublish

Résumé

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based

Identifiants

pubmed: 32431832
doi: 10.1107/S2052252520004030
pii: fq5010
pmc: PMC7201287
doi:

Types de publication

Journal Article

Langues

eng

Pagination

490-499

Subventions

Organisme : NIGMS NIH HHS
ID : R35 GM128867
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008496
Pays : United States

Informations de copyright

© Gallagher-Jones et al. 2020.

Références

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42
pubmed: 21460441
Microsc Microanal. 2019 Jun;25(3):563-582
pubmed: 31084643
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):848-53
pubmed: 9757100
Nature. 2007 May 24;447(7143):453-7
pubmed: 17468747
Curr Opin Struct Biol. 2012 Oct;22(5):602-12
pubmed: 23021872
Elife. 2013 Nov 19;2:e01345
pubmed: 24252878
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):859-66
pubmed: 16855301
Sci Adv. 2019 Aug 07;5(8):eaax4621
pubmed: 31457106
Ultramicroscopy. 2015 Jan;148:87-93
pubmed: 25461585
IUCrJ. 2015 Jan 27;2(Pt 2):168-76
pubmed: 25866654
Acta Crystallogr A. 2008 Jan;64(Pt 1):112-22
pubmed: 18156677
Nat Methods. 2014 Sep;11(9):927-930
pubmed: 25086503
IUCrJ. 2019 Jan 15;6(Pt 2):178-188
pubmed: 30867915
Science. 2016 Feb 26;351(6276):969-72
pubmed: 26917770
Inorg Chem. 2018 Aug 20;57(16):10241-10248
pubmed: 30063352
Nat Methods. 2009 Sep;6(9):651-3
pubmed: 19684596
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2019 Aug 1;75(Pt 4):495-504
pubmed: 32830707
Nature. 2007 Nov 15;450(7168):383-7
pubmed: 17952055
Science. 2019 May 17;364(6441):667-669
pubmed: 31097664
Structure. 2018 May 1;26(5):759-766.e4
pubmed: 29706530
Acta Crystallogr A Found Adv. 2016 Mar;72(Pt 2):236-42
pubmed: 26919375
Nat Commun. 2020 Feb 21;11(1):996
pubmed: 32081905
Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2652-66
pubmed: 25286849
Micron. 2016 Sep;88:30-6
pubmed: 27323282
Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12769-74
pubmed: 25136092
ACS Cent Sci. 2018 Nov 28;4(11):1587-1592
pubmed: 30555912
Acta Crystallogr A Found Adv. 2015 Jul;71(Pt 4):353-60
pubmed: 26131894
Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11232-11236
pubmed: 27647903
Nat Commun. 2015 Jun 01;6:7267
pubmed: 26028514
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
pubmed: 20124692
Nature. 2015 Sep 24;525(7570):486-90
pubmed: 26352473
Sci Rep. 2017 Sep 5;7(1):10409
pubmed: 28874736
Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):852-9
pubmed: 23633595
IUCrJ. 2015 Feb 03;2(Pt 2):246-55
pubmed: 25866661
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2019 Aug 1;75(Pt 4):523-531
pubmed: 32830710
Nat Mater. 2019 Aug;18(8):860-865
pubmed: 31160799
J Appl Crystallogr. 2018 Aug 09;51(Pt 5):1262-1273
pubmed: 30279637
J Appl Crystallogr. 2018 Nov 22;51(Pt 6):1652-1661
pubmed: 30546290
Commun Biol. 2019 Jan 18;2:26
pubmed: 30675524
IUCrJ. 2016 Jul 04;3(Pt 5):300-308
pubmed: 28461891

Auteurs

Marcus Gallagher-Jones (M)

Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.

Karen C Bustillo (KC)

National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA.

Colin Ophus (C)

National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA.

Logan S Richards (LS)

Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.

Jim Ciston (J)

National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA.

Sangho Lee (S)

Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.

Andrew M Minor (AM)

National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA.
Department of Materials Science and Engineering, University of California, Berkeley, California, USA.

Jose A Rodriguez (JA)

Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.

Classifications MeSH