1. Structural Biology and Molecular Biophysics
Download icon

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

  1. Dari Kimanius
  2. Björn O Forsberg
  3. Sjors HW Scheres  Is a corresponding author
  4. Erik Lindahl  Is a corresponding author
  1. Stockholm University, Sweden
  2. MRC Laboratory of Molecular Biology,, United Kingdom
Tools and Resources
  • Cited 525
  • Views 8,344
  • Annotations
Cite this article as: eLife 2016;5:e18722 doi: 10.7554/eLife.18722

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.

Article and author information

Author details

  1. Dari Kimanius

    Department of Biochemistry and Biophysics, Science for Life Laboratory,, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.

  2. Björn O Forsberg

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
    Competing interests
    No competing interests declared.

  3. 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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0462-6540

  4. 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.
    ORCID icon "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.

Reviewing Editor

  1. Sriram Subramaniam, National Cancer Institute, United States

Publication history

  1. Received: June 11, 2016
  2. Accepted: November 14, 2016
  3. Accepted Manuscript published: November 15, 2016 (version 1)
  4. Version of Record published: February 15, 2017 (version 2)

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.

Metrics

  • 8,344
    Page views
  • 1,863
    Downloads
  • 525
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Further reading

    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Molecular basis for functional connectivity between the voltage sensor and the selectivity filter gate in Shaker K+ channels

    Carlos A Z Bassetto Jnr et al.
    Research Article

    In Shaker K+ channels, the S4-S5 linker couples the voltage sensor (VSD) and pore domain (PD). Another coupling mechanism is revealed using two W434F-containing channels: L361R:W434F and L366H:W434F. In L361R:W434F, W434F affects the L361R VSD seen as a shallower Q-V curve that crosses the G-V. In L366H:W434F, L366H relieves the W434F effect converting a non-conductive channel in a conductive one. We report a chain of residues connecting the VSD (S4) to the selectivity filter (SF) in the PD of an adjacent subunit as the molecular basis for voltage-sensor selectivity filter gate (VS-SF) coupling. Single alanine substitutions in this region (L409A, S411A, S412A or F433A) are enough to disrupt the VS-SF coupling, shown by the absence of Q-V and G-V crossing in L361R:W434F mutant and by the lack of ionic conduction in the L366H:W434F mutant. This residue chain defines a new coupling between the VSD and the PD in voltage-gated channels.

    1. Structural Biology and Molecular Biophysics

    A critical residue in the α1M2–M3 linker regulating mammalian GABAA receptor pore gating by diazepam

    Joseph W Nors et al.
    Research Article Updated

    Benzodiazepines (BZDs) are a class of widely prescribed psychotropic drugs that modulate activity of GABAA receptors (GABAARs), neurotransmitter-gated ion channels critical for synaptic transmission. However, the physical basis of this modulation is poorly understood. We explore the role of an important gating domain, the α1M2–M3 linker, in linkage between the BZD site and pore gate. To probe energetics of this coupling without complication from bound agonist, we use a gain of function mutant (α1L9'Tβ2γ2L) directly activated by BZDs. We identify a specific residue whose mutation (α1V279A) more than doubles the energetic contribution of the BZD positive modulator diazepam (DZ) to pore opening and also enhances DZ potentiation of GABA-evoked currents in a wild-type background. In contrast, other linker mutations have little effect on DZ efficiency, but generally impair unliganded pore opening. Our observations reveal an important residue regulating BZD-pore linkage, thereby shedding new light on the molecular mechanism of these drugs.

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Pre-existing bilayer stresses modulate triglyceride accumulation in the ER versus lipid droplets

    Valeria Zoni et al.
    Research Article Updated

    Cells store energy in the form of neutral lipids (NLs) packaged into micrometer-sized organelles named lipid droplets (LDs). These structures emerge from the endoplasmic reticulum (ER) at sites marked by the protein seipin, but the mechanisms regulating their biogenesis remain poorly understood. Using a combination of molecular simulations, yeast genetics, and fluorescence microscopy, we show that interactions between lipids’ acyl-chains modulate the propensity of NLs to be stored in LDs, in turn preventing or promoting their accumulation in the ER membrane. Our data suggest that diacylglycerol, which is enriched at sites of LD formation, promotes the packaging of NLs into LDs, together with ER-abundant lipids, such as phosphatidylethanolamine. On the opposite end, short and saturated acyl-chains antagonize fat storage in LDs and promote accumulation of NLs in the ER. Our results provide a new conceptual understanding of LD biogenesis in the context of ER homeostasis and function.