1. Structural Biology and Molecular Biophysics
  2. Cell Biology
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The structure of the COPI coat determined within the cell

  1. Yury S Bykov
  2. Miroslava Schaffer
  3. Svetlana O Dodonova
  4. Sahradha Albert
  5. Jürgen M Plitzko
  6. Wolfgang Baumeister  Is a corresponding author
  7. Benjamin D Engel  Is a corresponding author
  8. John AG Briggs  Is a corresponding author
  1. European Molecular Biology Laboratory, Germany
  2. Max Planck Institute of Biochemistry, Germany
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Cite this article as: eLife 2017;6:e32493 doi: 10.7554/eLife.32493

Abstract

COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with in vitro reconstitution systems using purified components. In a previous paper (Dodonova et al., 2017), we determined a complete structural model of the in vitro reconstituted COPI coat. Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells. The native algal structure resembles the in vitro mammalian structure, but additionally reveals cargo bound beneath β'-COP. We find that all coat components disassemble simultaneously and relatively rapidly after budding. Structural analysis in situ, maintaining Golgi topology, shows that vesicles change their size, membrane thickness, and cargo content as they progress from cis to trans, but the structure of the coat machinery remains constant.

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The following previously published data sets were used

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Author details

  1. Yury S Bykov

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2959-4108
  2. Miroslava Schaffer

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Svetlana O Dodonova

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5002-8138
  4. Sahradha Albert

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Jürgen M Plitzko

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6402-8315
  6. Wolfgang Baumeister

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    For correspondence
    baumeist@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
  7. Benjamin D Engel

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    For correspondence
    engelben@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0941-4387
  8. John AG Briggs

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    For correspondence
    jbriggs@mrc-lmb.cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3990-6910

Funding

Deutsche Forschungsgemeinschaft (SFB1129 (Z2))

  • John AG Briggs

Deutsche Forschungsgemeinschaft (SFB-1035/Project A01)

  • Wolfgang Baumeister

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Margaret S. Robinson, University of Cambridge, United Kingdom

Publication history

  1. Received: October 4, 2017
  2. Accepted: November 16, 2017
  3. Accepted Manuscript published: November 17, 2017 (version 1)
  4. Version of Record published: December 5, 2017 (version 2)

Copyright

© 2017, Bykov 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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    Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.