9R09 | pdb_00009r09

Structure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 5.7

• PDB DOI: https://doi.org/10.2210/pdb9R09/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vaccinia virus Western Reserve, Vicugna pacos
• Expression System: Drosophila melanogaster, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-24 Released: 2025-09-03 
• Deposition Author(s): Vernuccio, R., Meola, A., Guardado-Calvo, P.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental, in silico

Literature

Structural basis of poxvirus fusion regulation and anti-A16/G9 antibody-mediated neutralization and protection.

Meola, A., Vernuccio, R., Battini, L., Albericio, G., Delgado, P., Bamford, R., Pokorny, L., Broutin, M., Martinez Leon, A., Gallien, S., Gil, M., Noriega, M.A., Guivel-Benhassine, F., Porrot, F., Postal, J., Buchrieser, J., Hubert, M., Haouz, A., Lafaye, P., Esteban, M., Hub, J.S., Mahevas, M., Chappert, P., Mercer, J., Garcia-Arriaza, J., Schwartz, O., Guardado-Calvo, P.

(2025) Cell 188: 6266

• PubMed: 40865523 
• DOI: https://doi.org/10.1016/j.cell.2025.07.040
• Primary Citation Related Structures: 
  9HBK, 9HL2, 9HLS, 9HNG, 9HPA, 9R09, 9R0B, 9R0J, 9RDH


• PubMed Abstract: 
  

  Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral fusion to the cell membrane. The EFC is a promising therapeutic target, but the absence of structural data has limited the development of fusion-inhibiting treatments. Here, we investigated A16/G9, a subcomplex of the EFC that controls fusion timing. Using cryo-electron microscopy, we showed how A16/G9 interacts with A56/K2, a viral fusion suppressor that prevents superinfection. Immunization with A16/G9 elicited a protective immune response in mice. Using X-ray crystallography, we characterized two neutralizing antibodies and engineered a chimeric antibody that cross-neutralizes several poxviruses more efficiently than 7D11, the most potent antibody targeting the EFC described to date. These findings highlight the potential of A16/G9 as a candidate for subunit vaccines and identify regions of the EFC as targets for antiviral development.

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Organizational Affiliation: 
• Structural biology of infectious diseases G5+ unit, Institut Pasteur, Université Paris Cité, Paris, France.
Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK; Medical Research Council, LMCB, University College London, London WC1E 6BT, UK.
Institut Necker Enfants Malades (INEM), Université Paris Cite, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir, Team Auto-Immune and Immune B cells, Paris, France.
Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, AP-HP, Université Paris Est Créteil (UPEC), Créteil, France.
Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, Paris, France; Vaccine Research Institute, Créteil, France.
Crystallography Platform-C2RT, Institut Pasteur, CNRS UMR3528, Université de Paris, Paris, France.
Antibody Engineering Platform, C2RT, Université de Paris Cité, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France.
Institut Necker Enfants Malades (INEM), Université Paris Cite, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir, Team Auto-Immune and Immune B cells, Paris, France; Université Paris Est-Creteil, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Team 2, Créteil, France.
Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.
Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
Structural biology of infectious diseases G5+ unit, Institut Pasteur, Université Paris Cité, Paris, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 95.9 kDa 
• Atom Count: 5,701 
• Modeled Residue Count: 678 
• Deposited Residue Count: 846 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion membrane protein OPG143	A	358	Vaccinia virus Western Reserve	Mutation(s): 0  Gene Names: OPG143, VACWR136, A16L
UniProt
Find proteins for P16710 (Vaccinia virus (strain Western Reserve)) Explore P16710  Go to UniProtKB:  P16710

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Entry-fusion complex protein OPG094	B	334	Vaccinia virus Western Reserve	Mutation(s): 0  Gene Names: OPG094, VACWR087, G9R
UniProt
Find proteins for P07611 (Vaccinia virus (strain Western Reserve)) Explore P07611  Go to UniProtKB:  P07611

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH D07	C [auth J000]	154	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES (Subject of Investigation/LOI)	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.558	α = 90
b = 147.066	β = 90
c = 183.138	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Vernuccio, R., Meola, A., Guardado-Calvo, P.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-22-CE11-0003

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references
• Version 1.2: 2025-11-12
  Changes: Database references