7VGR | pdb_00007vgr

SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab

• PDB DOI: https://doi.org/10.2210/pdb7VGR/pdb
• EM Map EMD-31977: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Mus musculus, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2021-09-18 Released: 2022-08-03 
• Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of SARS-CoV-2 membrane protein essential for virus assembly.

Zhang, Z., Nomura, N., Muramoto, Y., Ekimoto, T., Uemura, T., Liu, K., Yui, M., Kono, N., Aoki, J., Ikeguchi, M., Noda, T., Iwata, S., Ohto, U., Shimizu, T.

(2022) Nat Commun 13: 4399-4399

• PubMed: 35931673 
• DOI: https://doi.org/10.1038/s41467-022-32019-3
• Primary Citation Related Structures: 
  7VGR, 7VGS


• PubMed Abstract: 
  

  The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Japan.
Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.
Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.
CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, Japan.
Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, Japan.
RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. [e-mail].
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 154.79 kDa 
• Atom Count: 9,872 
• Modeled Residue Count: 1,272 
• Deposited Residue Count: 1,400 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YN7756_1 Fab light chain	A [auth C], C [auth E]	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YN7756_1 Fab heavy chain	B [auth D], D [auth F]	236	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein	E [auth A], F [auth B]	246	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0DTC5 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC5  Go to UniProtKB:  P0DTC5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary
• Version 1.3: 2025-06-25
  Changes: Data collection