Literature DB >> 25278130

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

Melody G Campbell, Bradley M Kearney, Anchi Cheng, Clinton S Potter, John E Johnson, Bridget Carragher, David Veesler.   

Abstract

A new era has begun for single particle cryo-electron microscopy (cryoEM) which can now compete with X-ray crystallography for determination of protein structures. The development of direct detectors constitutes a revolution that has led to a wave of near-atomic resolution cryoEM reconstructions. However, regardless of the sample studied, virtually all high-resolution reconstructions reported to date have been achieved using high-end microscopes. We demonstrate that the new generation of direct detectors coupled to a widely used mid-range electron microscope also enables obtaining cryoEM maps of sufficient quality for de novo modeling of protein structures of different sizes and symmetries. We provide an outline of the strategy used to achieve a 3.7 Å resolution reconstruction of Nudaurelia capensis ω virus and a 4.2 Å resolution reconstruction of the Thermoplasma acidophilum T20S proteasome.

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Year:  2014        PMID: 25278130      PMCID: PMC4497823          DOI: 10.1016/j.jsb.2014.09.008

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


  36 in total

1.  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

2.  Image processing for electron microscopy single-particle analysis using XMIPP.

Authors:  Sjors H W Scheres; Rafael Núñez-Ramírez; Carlos O S Sorzano; José María Carazo; Roberto Marabini
Journal:  Nat Protoc       Date:  2008       Impact factor: 13.491

3.  Structure of the yeast mitochondrial large ribosomal subunit.

Authors:  Alexey Amunts; Alan Brown; Xiao-Chen Bai; Jose L Llácer; Tanweer Hussain; Paul Emsley; Fei Long; Garib Murshudov; Sjors H W Scheres; V Ramakrishnan
Journal:  Science       Date:  2014-03-28       Impact factor: 47.728

4.  The refined structure of Nudaurelia capensis omega virus reveals control elements for a T = 4 capsid maturation.

Authors:  Charlotte Helgstrand; Sanjeev Munshi; John E Johnson; Lars Liljas
Journal:  Virology       Date:  2004-01-05       Impact factor: 3.616

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

Authors:  David Veesler; Melody G Campbell; Anchi Cheng; Chi-Yu Fu; Zachary Murez; John E Johnson; Clinton S Potter; Bridget Carragher
Journal:  J Struct Biol       Date:  2013-09-12       Impact factor: 2.867

6.  Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.

Authors:  Israel S Fernández; Xiao-Chen Bai; Garib Murshudov; Sjors H W Scheres; V Ramakrishnan
Journal:  Cell       Date:  2014-05-01       Impact factor: 41.582

7.  RELION: implementation of a Bayesian approach to cryo-EM structure determination.

Authors:  Sjors H W Scheres
Journal:  J Struct Biol       Date:  2012-09-19       Impact factor: 2.867

8.  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
Journal:  Nat Struct Mol Biol       Date:  2012-12-16       Impact factor: 15.369

9.  A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution.

Authors:  Xing Zhang; Huatao Guo; Lei Jin; Elizabeth Czornyj; Asher Hodes; Wong H Hui; Angela W Nieh; Jeff F Miller; Z Hong Zhou
Journal:  Elife       Date:  2013-12-17       Impact factor: 8.140

10.  Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.

Authors:  Wilson Wong; Xiao-chen Bai; Alan Brown; Israel S Fernandez; Eric Hanssen; Melanie Condron; Yan Hong Tan; Jake Baum; Sjors H W Scheres
Journal:  Elife       Date:  2014-06-09       Impact factor: 8.140

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  9 in total

1.  Best practices for managing large CryoEM facilities.

Authors:  Bart Alewijnse; Alun W Ashton; Melissa G Chambers; Songye Chen; Anchi Cheng; Mark Ebrahim; Edward T Eng; Wim J H Hagen; Abraham J Koster; Claudia S López; Natalya Lukoyanova; Joaquin Ortega; Ludovic Renault; Steve Reyntjens; William J Rice; Giovanna Scapin; Raymond Schrijver; Alistair Siebert; Scott M Stagg; Valerie Grum-Tokars; Elizabeth R Wright; Shenping Wu; Zhiheng Yu; Z Hong Zhou; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2017-08-04       Impact factor: 2.867

Review 2.  Cryo-EM of bacterial pili and archaeal flagellar filaments.

Authors:  Edward H Egelman
Journal:  Curr Opin Struct Biol       Date:  2017-06-10       Impact factor: 6.809

3.  Benchmarking cryo-EM Single Particle Analysis Workflow.

Authors:  Laura Y Kim; William J Rice; Edward T Eng; Mykhailo Kopylov; Anchi Cheng; Ashleigh M Raczkowski; Kelsey D Jordan; Daija Bobe; Clinton S Potter; Bridget Carragher
Journal:  Front Mol Biosci       Date:  2018-06-04

4.  High-speed high-resolution data collection on a 200 keV cryo-TEM.

Authors:  Jared V Peck; Jonathan F Fay; Joshua D Strauss
Journal:  IUCrJ       Date:  2022-01-29       Impact factor: 4.769

Review 5.  Unravelling biological macromolecules with cryo-electron microscopy.

Authors:  Rafael Fernandez-Leiro; Sjors H W Scheres
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

6.  2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy.

Authors:  Melody G Campbell; David Veesler; Anchi Cheng; Clinton S Potter; Bridget Carragher
Journal:  Elife       Date:  2015-03-11       Impact factor: 8.140

7.  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

8.  Structure of a Bacterial Virus DNA-Injection Protein Complex Reveals a Decameric Assembly with a Constricted Molecular Channel.

Authors:  Haiyan Zhao; Jeffrey A Speir; Tsutomu Matsui; Zihan Lin; Lingfei Liang; Anna Y Lynn; Brittany Varnado; Thomas M Weiss; Liang Tang
Journal:  PLoS One       Date:  2016-02-16       Impact factor: 3.240

9.  Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV.

Authors:  Mark A Herzik; Mengyu Wu; Gabriel C Lander
Journal:  Nat Methods       Date:  2017-10-09       Impact factor: 28.547

  9 in total

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