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PMID: 25486611 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Semi-automated selection of cryo-EM particles in RELION-1.3.

Journal of structural biology ·Vol. 189 ·No. 2 ·2015-02-00 ·Pages 114-22

Scheres SH

Abstract

The selection of particles suitable for high-resolution cryo-EM structure determination from noisy micrographs may represent a tedious and time-consuming step. Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION. At the heart of the procedure lies a fully CTF-corrected template-based picking algorithm, which is supplemented by a fast sorting algorithm and reference-free 2D class averaging to remove false positives. With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection. Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

Keywords
Automated particle picking Electron cryo-microscopy Single-particle analysis
MeSH Terms
Algorithms Cryoelectron Microscopy Hemocyanins/ultrastructure Imaging, Three-Dimensional Models, Molecular Protein Structure, Quaternary Software beta-Galactosidase/ultrastructure
Chemicals
Hemocyanins beta-Galactosidase keyhole-limpet hemocyanin
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Scheres Sjors H W
MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: scheres@mrc-lmb.cam.ac.uk.
References (38)
38 references, click to expand
  1. Structure of the yeast mitochondrial large ribosomal subunit.
    Science. 2014 Mar 28;343(6178):1485-9 PMID: 24675956
  2. Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
    Elife. 2014;3. doi: 10.7554/eLife.03080 PMID: 24913268
  3. Accurate determination of local defocus and specimen tilt in electron microscopy.
    J Struct Biol. 2003 Jun;142(3):334-47 PMID: 12781660
  4. Review: automatic particle detection in electron microscopy.
    J Struct Biol. 2001 Feb-Mar;133(2-3):90-101 PMID: 11472081
  5. Molecular architecture of a eukaryotic translational initiation complex.
    Science. 2013 Nov 15;342(6160):1240585 PMID: 24200810
  6. RELION: implementation of a Bayesian approach to cryo-EM structure determination.
    J Struct Biol. 2012 Dec;180(3):519-30 PMID: 23000701
  7. Automated particle picking for low-contrast macromolecules in cryo-electron microscopy.
    J Struct Biol. 2014 Apr;186(1):1-7 PMID: 24607413
  8. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
    Nat Methods. 2013 Jun;10(6):584-90 PMID: 23644547
  9. FindEM--a fast, efficient program for automatic selection of particles from electron micrographs.
    J Struct Biol. 2004 Jan-Feb;145(1-2):91-9 PMID: 15065677
  10. SIGNATURE: a single-particle selection system for molecular electron microscopy.
    J Struct Biol. 2007 Jan;157(1):168-73 PMID: 16870473
  11. Quantifying the local resolution of cryo-EM density maps.
    Nat Methods. 2014 Jan;11(1):63-5 PMID: 24213166
  12. Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.
    Elife. 2014;3:e01963 PMID: 24569482
  13. Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
    Cell. 2014 Jun 19;157(7):1632-43 PMID: 24930395
  14. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.
    Structure. 2012 Nov 7;20(11):1823-8 PMID: 23022349
  15. Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy.
    Ultramicroscopy. 2004 Nov;101(2-4):129-38 PMID: 15450658
  16. Automatic particle selection: results of a comparative study.
    J Struct Biol. 2004 Jan-Feb;145(1-2):3-14 PMID: 15065668
  17. Automated molecular microscopy: the new Leginon system.
    J Struct Biol. 2005 Jul;151(1):41-60 PMID: 15890530
  18. TRPV1 structures in distinct conformations reveal activation mechanisms.
    Nature. 2013 Dec 5;504(7478):113-8 PMID: 24305161
  19. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.
    Nat Methods. 2007 Jan;4(1):27-9 PMID: 17179934
  20. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.
    J Struct Biol. 2009 May;166(2):205-13 PMID: 19374019
  21. EMAN2: an extensible image processing suite for electron microscopy.
    J Struct Biol. 2007 Jan;157(1):38-46 PMID: 16859925
  22. Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise.
    Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):18037-41 PMID: 24106306
  23. Classification of structural heterogeneity by maximum-likelihood methods.
    Methods Enzymol. 2010;482:295-320 PMID: 20888966
  24. Three-dimensional structure of human γ-secretase.
    Nature. 2014 Aug 14;512(7513):166-70 PMID: 25043039
  25. Finding trimeric HIV-1 envelope glycoproteins in random noise.
    Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):E4175-7 PMID: 24106301
  26. Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli).
    Biochem Cell Biol. 2010 Oct;88(5):861-9 PMID: 20921997
  27. Particle finding in electron micrographs using a fast local correlation algorithm.
    Ultramicroscopy. 2003 Apr;94(3-4):225-36 PMID: 12524193
  28. Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.
    Curr Opin Struct Biol. 2011 Apr;21(2):265-73 PMID: 21333526
  29. Prevention of overfitting in cryo-EM structure determination.
    Nat Methods. 2012 Sep;9(9):853-4 PMID: 22842542
  30. A method for the alignment of heterogeneous macromolecules from electron microscopy.
    J Struct Biol. 2009 Apr;166(1):67-78 PMID: 19166941
  31. Detective quantum efficiency of electron area detectors in electron microscopy.
    Ultramicroscopy. 2009 Aug;109(9):1126-43 PMID: 19497671
  32. Automatic particle selection from electron micrographs using machine learning techniques.
    J Struct Biol. 2009 Sep;167(3):252-60 PMID: 19555764
  33. A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM.
    J Struct Biol. 2011 Sep;175(3):348-52 PMID: 21420497
  34. Molecular mechanism of antibody-mediated activation of β-galactosidase.
    Structure. 2014 Apr 8;22(4):621-7 PMID: 24613486
  35. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles.
    Elife. 2013;2:e00461 PMID: 23427024
  36. A Bayesian view on cryo-EM structure determination.
    J Mol Biol. 2012 Jan 13;415(2):406-18 PMID: 22100448
  37. Beam-induced motion correction for sub-megadalton cryo-EM particles.
    Elife. 2014;3:e03665 PMID: 25122622
  38. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.
    Ultramicroscopy. 2013 Dec;135:24-35 PMID: 23872039
Article Info
Journal
Journal of structural biology
Abbr.
J Struct Biol
ISSN
1095-8657
DOI
10.1016/j.jsb.2014.11.010
Email
scheres@mrc-lmb.cam.ac.uk
Published
2015-02-00
Epub
2014-00-06
Pages
114-22
Language
English
Region
United States
NLM ID
9011206
PMCID
PMC4318617
Subset
IM
Grants
Medical Research Council · MC_UP_A025_1013 · United Kingdom
External Links
PubMed source DOI: 10.1016/j.jsb.2014.11.010 PMC Full Text View journal details
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