9EXA | pdb_00009exa

SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A coronavirus assembly inhibitor that targets the viral membrane protein.

Laporte, M.Jochmans, D.Bardiot, D.Desmarets, L.Debski-Antoniak, O.J.Mizzon, G.Abdelnabi, R.Leyssen, P.Chiu, W.Zhang, Z.Nomura, N.Boland, S.Ohto, U.Stahl, Y.Wuyts, J.De Jonghe, S.Stevaert, A.van Hemert, M.J.Bontes, B.W.Wanningen, P.Groenewold, G.J.M.Zegar, A.Owczarek, K.Joshi, S.Koukni, M.Arzel, P.Klaassen, H.Vanherck, J.C.Vandecaetsbeek, I.Cremers, N.Donckers, K.Francken, T.Van Buyten, T.Rymenants, J.Schepers, J.Pyrc, K.Hilgenfeld, R.Dubuisson, J.Bosch, B.J.Van Kuppeveld, F.Eydoux, C.Decroly, E.Canard, B.Naesens, L.Weynand, B.Snijder, E.J.Belouzard, S.Shimizu, T.Bartenschlager, R.Hurdiss, D.L.Marchand, A.Chaltin, P.Neyts, J.

(2025) Nature 640: 514-523

  • DOI: https://doi.org/10.1038/s41586-025-08773-x
  • Primary Citation of Related Structures:  
    9EXA

  • PubMed Abstract: 

    The coronavirus membrane protein (M) is the main organizer of coronavirus assembly 1-3 . Here, we report on an M-targeting molecule, CIM-834, that blocks the assembly of SARS-CoV-2. CIM-834 was obtained through high-throughput phenotypic antiviral screening followed by medicinal-chemistry efforts and target elucidation. CIM-834 inhibits the replication of SARS-CoV-2 (including a broad panel of variants) and SARS-CoV. In SCID mice and Syrian hamsters intranasally infected with SARS-CoV-2, oral treatment reduced lung viral titres to nearly undetectable levels, even (as shown in mice) when treatment was delayed until 24 h before the end point. Treatment of infected hamsters prevented transmission to untreated sentinels. Transmission electron microscopy studies show that virion assembly is completely absent in cells treated with CIM-834. Single-particle cryo-electron microscopy reveals that CIM-834 binds and stabilizes the M protein in its short form, thereby preventing the conformational switch to the long form, which is required for successful particle assembly. In conclusion, we have discovered a new druggable target in the replication cycle of coronaviruses and a small molecule that potently inhibits it.


  • Organizational Affiliation
    • Virology, Antiviral Drug & Vaccine Research Group, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein
A, B
188Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC5 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC5 
Go to UniProtKB:  P0DTC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab-B light chain
C, E
218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab-B heavy chain
D, F
213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H7W (Subject of Investigation/LOI)
Query on A1H7W

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
6-[[1-[4,6-dimethyl-5-(2-methylpropyl)pyrimidin-2-yl]piperidin-4-yl]-methyl-amino]-N-(2-pyrrolidin-1-ylethyl)pyridazine-4-carboxamide
C27 H42 N8 O
BCMAYBORMJZUOR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland101005077
Netherlands Organisation for Scientific Research (NWO)Netherlands184.034.014

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.3: 2025-04-16
    Changes: Data collection, Database references