Literature DB >> 24036281

Maximizing the potential of electron cryomicroscopy data collected using direct detectors.

David Veesler1,2, Melody G Campbell1,2, Anchi Cheng1,2, Chi-Yu Fu1, Zachary Murez3, John E Johnson1, Clinton S Potter1,2, Bridget Carragher1,2.   

Abstract

Single-particle electron cryomicroscopy is undergoing a technical revolution due to the recent developments of direct detectors. These new recording devices detect electrons directly (i.e. without conversion into light) and feature significantly improved detective quantum efficiencies and readout rates as compared to photographic films or CCDs. We evaluated here the potential of one such detector (Gatan K2 Summit) to enable the achievement of near-atomic resolution reconstructions of biological specimens when coupled to a widely used, mid-range transmission electron microscope (FEI TF20 Twin). Compensating for beam-induced motion and stage drift provided a 4.4Å resolution map of Sulfolobus turreted icosahedral virus (STIV), which we used as a test particle in this study. Several motion correction and dose fractionation procedures were explored and we describe their influence on the resolution of the final reconstruction. We also compared the quality of this data to that collected with a FEI Titan Krios microscope equipped with a Falcon I direct detector, which provides a benchmark for data collected using a high-end electron microscope.
Copyright © 2013 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Direct detectors; Electron microscopy; Near-atomic resolution; Sulfolobus turreted icosahedral virus

Mesh:

Substances:

Year:  2013        PMID: 24036281      PMCID: PMC3832241          DOI: 10.1016/j.jsb.2013.09.003

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  39 in total

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Authors:  Peter B Rosenthal; Richard Henderson
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2.  Accurate determination of local defocus and specimen tilt in electron microscopy.

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Journal:  J Struct Biol       Date:  2003-06       Impact factor: 2.867

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4.  FREALIGN: high-resolution refinement of single particle structures.

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Journal:  J Struct Biol       Date:  2006-06-02       Impact factor: 2.867

5.  Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

Authors:  Xing Zhang; Ethan Settembre; Chen Xu; Philip R Dormitzer; Richard Bellamy; Stephen C Harrison; Nikolaus Grigorieff
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-31       Impact factor: 11.205

6.  Structure of Sputnik, a virophage, at 3.5-Å resolution.

Authors:  Xinzheng Zhang; Siyang Sun; Ye Xiang; Jimson Wong; Thomas Klose; Didier Raoult; Michael G Rossmann
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-22       Impact factor: 11.205

7.  The architecture and chemical stability of the archaeal Sulfolobus turreted icosahedral virus.

Authors:  Reza Khayat; Chi-yu Fu; Alice C Ortmann; Mark J Young; John E Johnson
Journal:  J Virol       Date:  2010-06-30       Impact factor: 5.103

8.  Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks.

Authors:  Hongrong Liu; Lei Jin; Sok Boon S Koh; Ivo Atanasov; Stan Schein; Lily Wu; Z Hong Zhou
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9.  Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.

Authors:  David Veesler; Thiam-Seng Ng; Anoop K Sendamarai; Brian J Eilers; C Martin Lawrence; Shee-Mei Lok; Mark J Young; John E Johnson; Chi-yu Fu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-21       Impact factor: 11.205

10.  Cryo-EM structure of the mature dengue virus at 3.5-Å resolution.

Authors:  Xiaokang Zhang; Peng Ge; Xuekui Yu; Jennifer M Brannan; Guoqiang Bi; Qinfen Zhang; Stan Schein; Z Hong Zhou
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  11 in total

1.  Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0.

Authors:  Po-Lin Chiu; Xueming Li; Zongli Li; Brian Beckett; Axel F Brilot; Nikolaus Grigorieff; David A Agard; Yifan Cheng; Thomas Walz
Journal:  J Struct Biol       Date:  2015-08-28       Impact factor: 2.867

Review 2.  Cryo-EM in drug discovery: achievements, limitations and prospects.

Authors:  Jean-Paul Renaud; Ashwin Chari; Claudio Ciferri; Wen-Ti Liu; Hervé-William Rémigy; Holger Stark; Christian Wiesmann
Journal:  Nat Rev Drug Discov       Date:  2018-06-08       Impact factor: 84.694

3.  Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.

Authors:  Sumudu P Leelananda; Steffen Lindert
Journal:  J Chem Theory Comput       Date:  2017-09-26       Impact factor: 6.006

4.  Structure and Immune Recognition of the HIV Glycan Shield.

Authors:  Max Crispin; Andrew B Ward; Ian A Wilson
Journal:  Annu Rev Biophys       Date:  2018-03-29       Impact factor: 12.981

5.  Near-atomic resolution reconstructions using a mid-range electron microscope operated at 200 kV.

Authors:  Melody G Campbell; Bradley M Kearney; Anchi Cheng; Clinton S Potter; John E Johnson; Bridget Carragher; David Veesler
Journal:  J Struct Biol       Date:  2014-09-30       Impact factor: 2.867

Review 6.  High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.

Authors:  Andreas Hoenger
Journal:  Protoplasma       Date:  2014-01-05       Impact factor: 3.356

7.  Symmetry-mismatch reconstruction of genomes and associated proteins within icosahedral viruses using cryo-EM.

Authors:  Xiaowu Li; Hongrong Liu; Lingpeng Cheng
Journal:  Biophys Rep       Date:  2016-05-27

8.  Methods to account for movement and flexibility in cryo-EM data processing.

Authors:  S Rawson; M G Iadanza; N A Ranson; S P Muench
Journal:  Methods       Date:  2016-03-24       Impact factor: 3.608

9.  Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy.

Authors:  Alexandra Walls; M Alejandra Tortorici; Berend-Jan Bosch; Brandon Frenz; Peter J M Rottier; Frank DiMaio; Felix A Rey; David Veesler
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Review 10.  Cryo electron microscopy to determine the structure of macromolecular complexes.

Authors:  Marta Carroni; Helen R Saibil
Journal:  Methods       Date:  2015-11-27       Impact factor: 3.608

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