New tools for automated high-resolution cryo-EM structure determination in RELION-3

  1. Jasenko Zivanov
  2. Takanori Nakane
  3. Björn O Forsberg
  4. Dari Kimanius
  5. Wim JH Hagen
  6. Erik Lindahl  Is a corresponding author
  7. Sjors HW Scheres  Is a corresponding author
  1. MRC Laboratory of Molecular Biology, United Kingdom
  2. Stockholm University, Sweden
  3. European Molecular Biology Laboratory, Germany

Abstract

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher-resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions.

Data availability

We mostly use publicly available data sets from the EMPIAR data base at EMBL-EBI. For this study, we have submitted to this data base our own data on the human gamma-secretase complex (EMPIAR-10194) and on the high-resolution apo-ferritin sample described in the text (EMPIAR-10200).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Jasenko Zivanov

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  2. 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
  3. Björn O Forsberg

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  4. Dari Kimanius

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  5. Wim JH Hagen

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6229-2692
  6. Erik Lindahl

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    For correspondence
    erik.lindahl@scilifelab.se
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2734-2794
  7. 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

Swiss National Science Foundation (SNF: P2BSP2 168735)

  • Jasenko Zivanov

Swedish Research Council (2017-04641)

  • Erik Lindahl

Knut och Alice Wallenbergs Stiftelse

  • Erik Lindahl

Japan Society for the Promotion of Science (Overseas Research Fellowship)

  • Takanori Nakane

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

Publication history

  1. Received: September 19, 2018
  2. Accepted: November 6, 2018
  3. Accepted Manuscript published: November 9, 2018 (version 1)
  4. Version of Record published: November 22, 2018 (version 2)

Copyright

© 2018, 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. Jasenko Zivanov
  2. Takanori Nakane
  3. Björn O Forsberg
  4. Dari Kimanius
  5. Wim JH Hagen
  6. Erik Lindahl
  7. Sjors HW Scheres
(2018)
New tools for automated high-resolution cryo-EM structure determination in RELION-3
eLife 7:e42166.
https://doi.org/10.7554/eLife.42166
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