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

Abstract
Data availability
Article and author information
Metrics

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

1. Bai XC
2. Scheres SHW
3. Bai XC
4. Yan C
5. Yang G
6. Lu P
7. Ma D
8. Sun L
9. Zhou R
10. Scheres SHW
11. Shi Y
(2018) 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.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10194/
(2018) Human apo-ferritin reconstructed in RELION-3.0
Electron Microscopy Public Image Archive, EMPIAR-10200.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10200/

The following previously published data sets were used

1. Bartesaghi A
2. Merk A
3. Banerjee S
4. Matthies D
5. Wu X
6. Milne JL
7. Subramaniam S
(2015) 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor
Electron Microscopy Public Image Archive, EMPIAR-10061.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10061/
1. Tan YZ
2. Lyumkis D
(2017) 40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin Trimer
Electron Microscopy Public Image Archive, EMPIAR-10097.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10097/
1. Chen DH
2. Afonine PV
3. Jakana J
4. Wang Z
5. Haase-Pettingell C
6. Jiang W
7. Adams PD
8. King JA
9. Schmid MF
10. Chiu W
(2017) Bacteriophage P22 mature virion capsid protein
Electron Microscopy Public Image Archive, EMPIAR-10083.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10083/

Article and author information

Author details

Jasenko Zivanov

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

Competing interests
No competing interests declared.
Takanori Nakane

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-2697-2767
Björn O Forsberg

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden

Competing interests
No competing interests declared.
Dari Kimanius

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden

Competing interests
No competing interests declared.
Wim JH Hagen

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-6229-2692
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.

"This ORCID iD identifies the author of this article:" 0000-0002-2734-2794
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.

"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.

Copyright

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.