A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0

  1. Jasenkio Zivanov  Is a corresponding author
  2. Joaquín Otón
  3. Zunlong Ke
  4. Andriko von Kügelgen
  5. Euan Pyle
  6. Kun Qu
  7. Dustin Morado
  8. Daniel Castaño-Díez
  9. Giulia Zanetti
  10. Tanmay AM Bharat
  11. John AG Briggs
  12. Sjors HW Scheres  Is a corresponding author
  1. MRC Laboratory of Molecular Biology, United Kingdom
  2. ALBA Synchrotron, Spain
  3. Birkbeck, University of London, United Kingdom
  4. University of Basel, Switzerland

Abstract

We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt series alignments, beam-induced motions of the particles throughout the tilt series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, in particular for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.

Data availability

We have only used previously published cryo-EM data sets for testing our software.Reconstructed maps and atomic models generated in this study have been submitted to the EMDB and PDB, with entry codes as indicated in Table 1.

The following previously published data sets were used

Article and author information

Author details

  1. Jasenkio Zivanov

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    For correspondence
    jasenko.zivanov@gmail.com
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8407-0759
  2. Joaquín Otón

    ALBA Synchrotron, Cerdanyola del Vallès, Spain
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2195-4730
  3. Zunlong Ke

    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:" 0000-0002-8408-850X
  4. Andriko von Kügelgen

    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:" 0000-0002-0017-2414
  5. Euan Pyle

    Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4633-4917
  6. Kun Qu

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  7. Dustin Morado

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  8. Daniel Castaño-Díez

    University of Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
  9. Giulia Zanetti

    Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
    Competing interests
    Giulia Zanetti, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1905-0342
  10. Tanmay AM Bharat

    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:" 0000-0002-0168-0277
  11. John AG Briggs

    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:" 0000-0003-3990-6910
  12. 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

UK Research and Innovation (MC_UP_A025_1013)

  • Sjors HW Scheres

UK Research and Innovation (MC_UP_1201/16)

  • John AG Briggs

European Research Council (ERC-CoG-2014 grant 648432)

  • John AG Briggs

European Research Council (ERC-StG-2019 grant 852915)

  • Giulia Zanetti

Swiss National Science Foundation (205321_179041/1)

  • Daniel Castaño-Díez

UK Research and Innovation (BBSRC grant BB/T002670/1)

  • Giulia Zanetti

European Research Council (ERC-AdG-2015 grant 692726)

  • Jasenkio Zivanov

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

Reviewing Editor

  1. Edward H Egelman, University of Virginia, United States

Version history

  1. Preprint posted: February 28, 2022 (view preprint)
  2. Received: September 26, 2022
  3. Accepted: December 4, 2022
  4. Accepted Manuscript published: December 5, 2022 (version 1)
  5. Accepted Manuscript updated: December 6, 2022 (version 2)
  6. Version of Record published: January 5, 2023 (version 3)

Copyright

© 2022, Zivanov 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. Jasenkio Zivanov
  2. Joaquín Otón
  3. Zunlong Ke
  4. Andriko von Kügelgen
  5. Euan Pyle
  6. Kun Qu
  7. Dustin Morado
  8. Daniel Castaño-Díez
  9. Giulia Zanetti
  10. Tanmay AM Bharat
  11. John AG Briggs
  12. Sjors HW Scheres
(2022)
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
eLife 11:e83724.
https://doi.org/10.7554/eLife.83724

Share this article

https://doi.org/10.7554/eLife.83724

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