Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

  1. Takanori Nakane
  2. Dari Kimanius
  3. Erik Lindahl
  4. Sjors HW Scheres  Is a corresponding author
  1. MRC Laboratory of Molecular Biology, United Kingdom
  2. Stockholm University, Sweden

Abstract

Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.

Data availability

The spliceosome and ribosome datasets have been uploaded to the EMPIAR database. Their entry numebrs are 10180 and 10028 respectively

The following data sets were generated

Article and author information

Author details

  1. Takanori Nakane

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2697-2767
  2. Dari Kimanius

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  3. Erik Lindahl

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2734-2794
  4. Sjors HW Scheres

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    For correspondence
    scheres@mrc-lmb.cam.ac.uk
    Competing interests
    Sjors HW Scheres, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0462-6540

Funding

Medical Research Council (MC UP A025 1013)

  • Sjors HW Scheres

Svenska Forskningsrådet Formas (2017-04641)

  • Erik Lindahl

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Axel T Brunger, Stanford University Medical Center, United States

Version history

  1. Received: March 22, 2018
  2. Accepted: May 31, 2018
  3. Accepted Manuscript published: June 1, 2018 (version 1)
  4. Version of Record published: June 18, 2018 (version 2)

Copyright

© 2018, Nakane et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Takanori Nakane
  2. Dari Kimanius
  3. Erik Lindahl
  4. Sjors HW Scheres
(2018)
Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
eLife 7:e36861.
https://doi.org/10.7554/eLife.36861

Share this article

https://doi.org/10.7554/eLife.36861

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