Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

Abstract
Data availability
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Abstract

By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

Data availability

The following data sets were generated

(2016) RELION-2.0 reconstruction for beta-galactosidase data in EMPIAR-10061
Publicly available at the EBI Protein Data Bank in Europe (accession no: EMD-4116).

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-4116

The following previously published data sets were used

1. Scheres SH
(2014) Beta-galactosidase Falcon-II micrographs plus manually selected coordinates by Richard Henderson
Publicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10017).

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10017/
1. Wong W
2. Bai XC
3. Brown A
4. Fernandez IS
5. Hanssen E
6. Condron M
7. Tan YH
8. Baum J
9. Scheres SHW
(2014) Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Publicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10028).

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10028/
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
Publicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10061).

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10061/

Article and author information

Author details

Dari Kimanius

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

Competing interests
No competing interests declared.
Björn O Forsberg

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

Competing interests
No competing interests declared.
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
Erik Lindahl

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

For correspondence
erik.lindahl@dbb.su.se

Competing interests
No competing interests declared.

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

Funding

Medical Research Council (MC UP A025 1013)

Sjors HW Scheres

Vetenskapsrådet (2013-5901)

Erik Lindahl

Horizon 2020 (EINFRA-2015-1-675728)

Erik Lindahl

Swedish e-Science Research Centre

Erik Lindahl

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.