Structure of SARS-CoV-2 M protein in lipid nanodiscs

  1. Kimberly A Dolan
  2. Mandira Dutta
  3. David M Kern
  4. Abhay Kotecha
  5. Gregory A Voth
  6. Stephen G Brohawn  Is a corresponding author
  1. University of California, Berkeley, United States
  2. University of Chicago, United States
  3. Thermo Fisher Scientific, Netherlands

Abstract

SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity in a simple lipid bilayer and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.

Data availability

All data and reagents associated with this study are publicly available. The final model is in the PDB under 8CTK, the final map is in the EMDB under EMD-26993, and micrographs (original and motion corrected) and final particle stack are deposited in EMPIAR under 11067.

The following data sets were generated

Article and author information

Author details

  1. Kimberly A Dolan

    Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  2. Mandira Dutta

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
  3. David M Kern

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  4. Abhay Kotecha

    Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
    Competing interests
    Abhay Kotecha, is an employee of Thermo Fisher Scientific..
  5. Gregory A Voth

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3267-6748
  6. Stephen G Brohawn

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    brohawn@berkeley.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6768-3406

Funding

New York Stem Cell Foundation (R-N145)

  • Stephen G Brohawn

Fast Grants

  • Stephen G Brohawn

National Science Foundation

  • Kimberly A Dolan

National Science Foundation (CHE-2029092)

  • Mandira Dutta
  • Gregory A Voth

National Science Foundation (OAC-1818253)

  • Gregory A Voth

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

Reviewing Editor

  1. Owen Pornillos, University of Virginia, United States

Version history

  1. Preprint posted: June 13, 2022 (view preprint)
  2. Received: July 8, 2022
  3. Accepted: October 18, 2022
  4. Accepted Manuscript published: October 20, 2022 (version 1)
  5. Version of Record published: November 8, 2022 (version 2)

Copyright

© 2022, Dolan 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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  1. Kimberly A Dolan
  2. Mandira Dutta
  3. David M Kern
  4. Abhay Kotecha
  5. Gregory A Voth
  6. Stephen G Brohawn
(2022)
Structure of SARS-CoV-2 M protein in lipid nanodiscs
eLife 11:e81702.
https://doi.org/10.7554/eLife.81702

Share this article

https://doi.org/10.7554/eLife.81702

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