Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
- Stockholm University, Sweden
- MRC Laboratory of Molecular Biology,, United Kingdom
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
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RELION-2.0 reconstruction for beta-galactosidase data in EMPIAR-10061Publicly available at the EBI Protein Data Bank in Europe (accession no: EMD-4116).
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Beta-galactosidase Falcon-II micrographs plus manually selected coordinates by Richard HendersonPublicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10017).
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Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetinePublicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10028).
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2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitorPublicly available at the EBI Electron Microscopy Pilot Image Archive (accession no: EMPIAR-10061).
Article and author information
Author details
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
© 2016, Kimanius 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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Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
eLife 5:e18722.
https://doi.org/10.7554/eLife.18722
Further reading
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- Structural Biology and Molecular Biophysics
The calcium-activated TMEM16 proteins and the mechanosensitive/osmolarity-activated OSCA/TMEM63 proteins belong to the Transmembrane Channel/Scramblase (TCS) superfamily. Within the superfamily, OSCA/TMEM63 proteins, as well as TMEM16A and TMEM16B, are thought to function solely as ion channels. However, most TMEM16 members, including TMEM16F, maintain an additional function as scramblases, rapidly exchanging phospholipids between leaflets of the membrane. Although recent studies have advanced our understanding of TCS structure–function relationships, the molecular determinants of TCS ion and lipid permeation remain unclear. Here, we show that single mutations along the transmembrane helix (TM) 4/6 interface allow non-scrambling TCS members to permeate phospholipids. In particular, this study highlights the key role of TM 4 in controlling TCS ion and lipid permeation and offers novel insights into the evolution of the TCS superfamily, suggesting that, like TMEM16s, the OSCA/TMEM63 family maintains a conserved potential to permeate ions and phospholipids.
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- Structural Biology and Molecular Biophysics
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