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).
-
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.
-
Human apo-ferritin reconstructed in RELION-3.0Electron Microscopy Public Image Archive, EMPIAR-10200.
-
2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitorElectron Microscopy Public Image Archive, EMPIAR-10061.
-
40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin TrimerElectron Microscopy Public Image Archive, EMPIAR-10097.
-
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.
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.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
New tools for automated high-resolution cryo-EM structure determination in RELION-3
eLife 7:e42166.
https://doi.org/10.7554/eLife.42166
