New tools for automated high-resolution cryo-EM structure determination in RELION-3
- MRC Laboratory of Molecular Biology, United Kingdom
- Stockholm University, Sweden
- 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).
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An atomic structure of human gamma-secretase [2925 multi-frame micrographs composed of 20 frames each in MRCS format]Electron Microscopy Public Image Archive, EMPIAR-10194.
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Human apo-ferritin reconstructed in RELION-3.0Electron Microscopy Public Image Archive, EMPIAR-10200.
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2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitorElectron Microscopy Public Image Archive, EMPIAR-10061.
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40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin TrimerElectron Microscopy Public Image Archive, EMPIAR-10097.
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Bacteriophage P22 mature virion capsid proteinElectron Microscopy Public Image Archive, EMPIAR-10083.
Article and author information
Author details
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
- Edward H Egelman, University of Virginia, United States
Version history
- Received: September 19, 2018
- Accepted: November 6, 2018
- Accepted Manuscript published: November 9, 2018 (version 1)
- 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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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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