Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States; Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
Mandira Dutta
Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, United States
David M Kern
Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
Abhay Kotecha
Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, United States
Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
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.
