Literature DB >> 24106306

Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise.

Richard Henderson1.   

Abstract

Single particle cryo-electron microscopy is currently poised to produce high-resolution structures of many biological assemblies, but several pitfalls can trap the unwary. This critique highlights one problem that is particularly relevant when smaller structures are being studied. It is known as "Einstein from noise," in which the experimenter honestly believes they have recorded images of their particles, whereas in reality, most if not all of their data consist of pure noise. Selection of particles using cross-correlation methods can then lead to 3D maps that resemble the model used in the initial selection and provide the illusion of progress. Suggestions are given about how to circumvent the problem.

Entities:  

Keywords:  3DEM; EMDB; SPEM; cryo-EM; validation

Mesh:

Substances:

Year:  2013        PMID: 24106306      PMCID: PMC3831464          DOI: 10.1073/pnas.1314449110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  28 in total

1.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

Authors:  Peter B Rosenthal; Richard Henderson
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

2.  Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domains.

Authors:  Chikara Sato; Kozo Hamada; Toshihiko Ogura; Atsuo Miyazawa; Kenji Iwasaki; Yoko Hiroaki; Kazutoshi Tani; Akiko Terauchi; Yoshinori Fujiyoshi; Katsuhiko Mikoshiba
Journal:  J Mol Biol       Date:  2004-02-06       Impact factor: 5.469

3.  Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.

Authors:  Audray Harris; Mario J Borgnia; Dan Shi; Alberto Bartesaghi; Haifeng He; Robert Pejchal; Yun Kenneth Kang; Rafael Depetris; Andre J Marozsan; Rogier W Sanders; Per Johan Klasse; Jacqueline L S Milne; Ian A Wilson; William C Olson; John P Moore; Sriram Subramaniam
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-27       Impact factor: 11.205

4.  Cryo-electron microscopy of viruses.

Authors:  M Adrian; J Dubochet; J Lepault; A W McDowall
Journal:  Nature       Date:  1984 Mar 1-7       Impact factor: 49.962

5.  A method for the alignment of heterogeneous macromolecules from electron microscopy.

Authors:  Maxim Shatsky; Richard J Hall; Steven E Brenner; Robert M Glaeser
Journal:  J Struct Biol       Date:  2008-12-30       Impact factor: 2.867

6.  Prevention of overfitting in cryo-EM structure determination.

Authors:  Sjors H W Scheres; Shaoxia Chen
Journal:  Nat Methods       Date:  2012-09       Impact factor: 28.547

7.  Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.

Authors:  Richard Henderson; Shaoxia Chen; James Z Chen; Nikolaus Grigorieff; Lori A Passmore; Luciano Ciccarelli; John L Rubinstein; R Anthony Crowther; Phoebe L Stewart; Peter B Rosenthal
Journal:  J Mol Biol       Date:  2011-09-12       Impact factor: 5.469

8.  Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.

Authors:  Youdong Mao; Liping Wang; Christopher Gu; Alon Herschhorn; Shi-Hua Xiang; Hillel Haim; Xinzhen Yang; Joseph Sodroski
Journal:  Nat Struct Mol Biol       Date:  2012-08-05       Impact factor: 15.369

9.  De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy.

Authors:  Deryck J Mills; Stella Vitt; Mike Strauss; Seigo Shima; Janet Vonck
Journal:  Elife       Date:  2013-03-05       Impact factor: 8.140

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

Authors:  Xueming Li; Paul Mooney; Shawn Zheng; Christopher R Booth; Michael B Braunfeld; Sander Gubbens; David A Agard; Yifan Cheng
Journal:  Nat Methods       Date:  2013-05-05       Impact factor: 28.547

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  59 in total

1.  Single-particle electron microscopy in the study of membrane protein structure.

Authors:  Rita De Zorzi; Wei Mi; Maofu Liao; Thomas Walz
Journal:  Microscopy (Oxf)       Date:  2015-10-15       Impact factor: 1.571

2.  How good can cryo-EM become?

Authors:  Robert M Glaeser
Journal:  Nat Methods       Date:  2016-01       Impact factor: 28.547

Review 3.  Principles of cryo-EM single-particle image processing.

Authors:  Fred J Sigworth
Journal:  Microscopy (Oxf)       Date:  2015-12-24       Impact factor: 1.571

4.  The revolution will not be crystallized: a new method sweeps through structural biology.

Authors:  Ewen Callaway
Journal:  Nature       Date:  2015-09-10       Impact factor: 49.962

5.  Reply to Subramaniam, van Heel, and Henderson: Validity of the cryo-electron microscopy structures of the HIV-1 envelope glycoprotein complex.

Authors:  Youdong Mao; Luis R Castillo-Menendez; Joseph G Sodroski
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-05       Impact factor: 11.205

6.  Structure of trimeric HIV-1 envelope glycoproteins.

Authors:  Sriram Subramaniam
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-08       Impact factor: 11.205

7.  Crystal structure of a soluble cleaved HIV-1 envelope trimer.

Authors:  Jean-Philippe Julien; Albert Cupo; Devin Sok; Robyn L Stanfield; Dmitry Lyumkis; Marc C Deller; Per-Johan Klasse; Dennis R Burton; Rogier W Sanders; John P Moore; Andrew B Ward; Ian A Wilson
Journal:  Science       Date:  2013-10-31       Impact factor: 47.728

Review 8.  Challenges and opportunities in cryo-EM single-particle analysis.

Authors:  Dmitry Lyumkis
Journal:  J Biol Chem       Date:  2019-02-25       Impact factor: 5.157

9.  APPLE picker: Automatic particle picking, a low-effort cryo-EM framework.

Authors:  Ayelet Heimowitz; Joakim Andén; Amit Singer
Journal:  J Struct Biol       Date:  2018-08-19       Impact factor: 2.867

Review 10.  Single-Particle Cryo-EM at Crystallographic Resolution.

Authors:  Yifan Cheng
Journal:  Cell       Date:  2015-04-23       Impact factor: 41.582

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