9NZ3 | pdb_00009nz3

SARS-CoV M protein dimer in complex with JNJ-9676 and FAb B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into MERS and SARS coronavirus membrane proteins.

Mann, M.K.Yin, Y.Marsili, S.Xie, J.Doijen, J.Miller, R.Piassek, M.van den Broeck, N.Kariuki, C.K.de Gruyter, H.L.M.Leijs, A.A.Snijder, E.J.van Hemert, M.J.Keustermans, K.Van Gool, M.Yu, X.Loock, M.V.Koul, A.Sharma, S.Van Damme, E.Abeywickrema, P.

(2025) Commun Biol 8: 1651-1651

  • DOI: https://doi.org/10.1038/s42003-025-09042-3
  • Primary Citation of Related Structures:  
    9NZ3, 9NZ4, 9NZ5

  • PubMed Abstract: 

    The membrane (M) protein of coronaviruses is essential for maintaining structural integrity during membrane virion budding and viral pathogenesis. Given its high conservation in lineages within the betacoronavirus genus, such as sarbecoviruses, the M protein presents as an attractive therapeutic target; however, developing broad-spectrum antivirals targeting coronaviruses such as MERS-CoV is challenging due to lower sequence conservation and limited structural information available beyond that of the SARS-CoV-2 M protein. In this study, we report 3-3.2 Å resolution structures of MERS-CoV M protein, engineered with a SARS-CoV-2-like antibody interface, representing the first human merbecovirus M protein structure, and SARS-CoV M protein structures, with and without a previously identified SARS-CoV-2 M protein inhibitor, JNJ-9676. We highlight the structural differences between the MERS-CoV, SARS-CoV and SARS-CoV-2 M proteins, and present insights into the conservation of the JNJ-9676 binding pocket as well as key differences that could be targeted to accelerate the design of specific MERS-CoV and broad-spectrum antivirals targeting coronavirus M proteins.


  • Organizational Affiliation
    • Johnson and Johnson, Spring House, PA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein
A, B
269SARS-CoV-2 pseudovirusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAb B light chain
C, E
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAb B heavy chain
D, F
225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AE8 (Subject of Investigation/LOI)
Query on A1AE8

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
(6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide
C28 H21 F2 N5 O2
XXXBMVUCPXBZMT-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryos

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesHHSO100201700018C

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-10
    Changes: Data collection, Database references