Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM will facilitate determination of three-dimensional structures of smaller, lower-symmetry macromolecular complexes to higher resolution than pre...

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Bibliographic Details
Published in	Nature methods Vol. 10; no. 6; pp. 584 - 590
Main Authors	Li, Xueming, Mooney, Paul, Zheng, Shawn, Booth, Christopher R, Braunfeld, Michael B, Gubbens, Sander, Agard, David A, Cheng, Yifan
Format	Journal Article
Language	English
Published	New York Nature Publishing Group US 01.06.2013 Nature Publishing Group
Subjects	631/114/1314 631/1647/2258/1258/1259 631/1647/328/1259 631/45/612 Bioinformatics Biological Microscopy Biological Techniques Biomedical Engineering/Biotechnology Cryoelectron microscopy Cryoelectron Microscopy - methods Data acquisition Electrons Imaging, Three-Dimensional - methods Life Sciences Methods Microscopy Motion Proteasome Endopeptidase Complex - ultrastructure Proteins Proteomics Thermoplasma - enzymology Three-dimensional display systems United States
Online Access	Get full text
ISSN	1548-7091 1548-7105 1548-7105
DOI	10.1038/nmeth.2472

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Abstract	The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM will facilitate determination of three-dimensional structures of smaller, lower-symmetry macromolecular complexes to higher resolution than previously possible. In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron–counting detector, we confirmed that electron beam–induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency—key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.
AbstractList	The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM will facilitate determination of three-dimensional structures of smaller, lower-symmetry macromolecular complexes to higher resolution than previously possible. In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron–counting detector, we confirmed that electron beam–induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency—key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples. In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples. In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples. In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to 3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an 700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.
Audience	Academic
Author	Gubbens, Sander Agard, David A Cheng, Yifan Li, Xueming Braunfeld, Michael B Zheng, Shawn Booth, Christopher R Mooney, Paul
Author_xml	– sequence: 1 givenname: Xueming surname: Li fullname: Li, Xueming organization: Department of Biochemistry and Biophysics, The Keck Advanced Microscopy Laboratory, University of California, San Francisco (UCSF) – sequence: 2 givenname: Paul surname: Mooney fullname: Mooney, Paul organization: Gatan Inc – sequence: 3 givenname: Shawn surname: Zheng fullname: Zheng, Shawn organization: Department of Biochemistry and Biophysics, The Keck Advanced Microscopy Laboratory, University of California, San Francisco (UCSF), The Howard Hughes Medical Institute (HHMI), UCSF – sequence: 4 givenname: Christopher R surname: Booth fullname: Booth, Christopher R organization: Gatan Inc – sequence: 5 givenname: Michael B surname: Braunfeld fullname: Braunfeld, Michael B organization: Department of Biochemistry and Biophysics, The Keck Advanced Microscopy Laboratory, University of California, San Francisco (UCSF), The Howard Hughes Medical Institute (HHMI), UCSF – sequence: 6 givenname: Sander surname: Gubbens fullname: Gubbens, Sander organization: Gatan Inc – sequence: 7 givenname: David A surname: Agard fullname: Agard, David A email: agard@msg.ucsf.edu organization: Department of Biochemistry and Biophysics, The Keck Advanced Microscopy Laboratory, University of California, San Francisco (UCSF), The Howard Hughes Medical Institute (HHMI), UCSF – sequence: 8 givenname: Yifan surname: Cheng fullname: Cheng, Yifan email: ycheng@ucsf.edu organization: Department of Biochemistry and Biophysics, The Keck Advanced Microscopy Laboratory, University of California, San Francisco (UCSF)
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/23644547$$D View this record in MEDLINE/PubMed
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PublicationDate_xml	– month: 06 year: 2013 text: 2013-06-01 day: 01
PublicationDecade	2010
PublicationPlace	New York
PublicationPlace_xml	– name: New York – name: United States
PublicationSubtitle	Techniques for life scientists and chemists
PublicationTitle	Nature methods
PublicationTitleAbbrev	Nat Methods
PublicationTitleAlternate	Nat Methods
PublicationYear	2013
Publisher	Nature Publishing Group US Nature Publishing Group
Publisher_xml	– name: Nature Publishing Group US – name: Nature Publishing Group
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Snippet	The combination of a direct electron-detection camera that can count individual electrons and an algorithm for correcting for beam-induced motion in cryo-EM... In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution...
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SubjectTerms	631/114/1314 631/1647/2258/1258/1259 631/1647/328/1259 631/45/612 Bioinformatics Biological Microscopy Biological Techniques Biomedical Engineering/Biotechnology Cryoelectron microscopy Cryoelectron Microscopy - methods Data acquisition Electrons Imaging, Three-Dimensional - methods Life Sciences Methods Microscopy Motion Proteasome Endopeptidase Complex - ultrastructure Proteins Proteomics Thermoplasma - enzymology Three-dimensional display systems
Title	Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
URI	https://link.springer.com/article/10.1038/nmeth.2472 https://www.ncbi.nlm.nih.gov/pubmed/23644547 https://www.proquest.com/docview/1357394147 https://www.proquest.com/docview/1357498759
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