9EXA | pdb_00009exa

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

• PDB DOI: https://doi.org/10.2210/pdb9EXA/pdb
• EM Map EMD-50034: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
• Expression System: Homo sapiens, Mus musculus
• Mutation(s): No 


• Deposited: 2024-04-05 Released: 2025-01-22 
• Deposition Author(s): Debski-Antoniak, O.J., Hurdiss, D.L.
• Funding Organization(s): Innovative Medicines Initiative, Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

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

Starting Models: experimental, in silico

Literature

An orally efficacious coronavirus assembly inhibitor that targets the viral M 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., Bolland, S., Ohto, U., Stahl, Y., Wuyts, J., De Jonghe, S., Dubuisson, J., Bosch, B.J., van Kuppeveld, J.M., Eydoux, C., Decroly, E., Canard, B., Naesens, L., Snijder, E., Belouzard, S., Shimizu, T., Bartenschlager, R., Hurdiss, D.L., Marchand, A., Chaltin, P., Neyts, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 137.77 kDa 
• Atom Count: 9,700 
• Modelled Residue Count: 1,238 
• Deposited Residue Count: 1,238 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein	A, B	188	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC5 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC5  Go to UniProtKB:  P0DTC5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-B light chain	C, E	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-B heavy chain	D, F	213	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H7W (Subject of Investigation/LOI)	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:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Debski-Antoniak, O.J., Hurdiss, D.L.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	101005077
Netherlands Organisation for Scientific Research (NWO)	Netherlands	184.034.014

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release