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Multi-body Refinement of Cryo-EM Images in RELION

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cryoEM

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2215))

Abstract

Single-particle analysis of electron cryo-microscopy (cryo-EM) images allows structure determination of macromolecular complexes. But when these molecules adopt many different conformations, traditional image processing approaches often lead to blurred reconstructions. By considering complexes to be comprised of multiple, independently moving rigid bodies, multi-body refinement in RELION enables structure determination of highly flexible complexes, while at the same time providing a characterization of the motions in the complex. Here, we describe how to perform multi-body refinement in RELION using a publicly available example. We outline how to prepare the necessary files, how to run the actual multi-body calculation, and how to interpret its output. This method can be applied to any cryo-EM data set of flexible complexes that can be divided into two or more bodies, each with a minimum molecular weight of 100–150 kDa.

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Acknowledgments

We are grateful to Clemens Plaschka for discussions; to Jake Grimmett and Toby Darling for help with high-performance computing; and to Shabih Shakeel, Rafael Fernandez-Leiro, and Giulia Zanetti for critical reading of the manuscript. This study was supported by the MRC-LMB EM facility. Funding was provided by the UK Medical Research Council to SHWS (MC_UP_A025_1013); and the Japan Society for the Promotion of Science through an Overseas Research Fellowship to TN.

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Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK

    Takanori Nakane & Sjors H. W. Scheres

Authors
  1. Takanori Nakane
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  2. Sjors H. W. Scheres
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Corresponding author

Correspondence to Sjors H. W. Scheres .

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Editors and Affiliations

  1. Howard Hughes Medical Institute Departments of Biological Chemistry and Physiology, University of California, Los Angeles, Los Angeles, CA, USA

    Tamir Gonen

  2. Chemical Engineering, School for Engineering of Matter, Transport and Energy; Center for Applied Structural Discovery Biodesign Institute, Arizona State University, Tempe, AZ, USA

    Brent L. Nannenga

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Nakane, T., Scheres, S.H.W. (2021). Multi-body Refinement of Cryo-EM Images in RELION. In: Gonen, T., Nannenga, B.L. (eds) cryoEM. Methods in Molecular Biology, vol 2215. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0966-8_7

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  • DOI: https://doi.org/10.1007/978-1-0716-0966-8_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0965-1

  • Online ISBN: 978-1-0716-0966-8

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