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- PDB-9hbk: Structure of A16/G9 in complex with A56/K2 (vaccinia virus) -

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Basic information

Entry
Database: PDB / ID: 9hbk
TitleStructure of A16/G9 in complex with A56/K2 (vaccinia virus)
Components
  • Entry-fusion complex protein OPG094
  • Protein OPG185
  • Superinfection exclusion protein
  • Virion membrane protein OPG143
KeywordsVIRAL PROTEIN / poxvirus / viral fusion / vaccinia virus / mpox virus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell membrane / serine-type endopeptidase inhibitor activity / DNA-templated transcription termination / helicase activity / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane ...membrane fusion involved in viral entry into host cell / host cell membrane / serine-type endopeptidase inhibitor activity / DNA-templated transcription termination / helicase activity / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular space / DNA binding / ATP binding / membrane
Similarity search - Function
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Immunoglobulin V-set domain ...Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Entry-fusion complex protein OPG094 / Virion membrane protein OPG143 / Superinfection exclusion protein / Protein OPG185
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsVernuccio, R. / Meola, A. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 France
CitationJournal: Cell / Year: 2025
Title: Structural basis of poxvirus fusion regulation and anti-A16/G9 antibody-mediated neutralization and protection.
Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien ...Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien / María Gil / María A Noriega / Florence Guivel-Benhassine / Françoise Porrot / Jeanne Postal / Julian Buchrieser / Mathieu Hubert / Ahmed Haouz / Pierre Lafaye / Mariano Esteban / Jochen S Hub / Matthieu Mahévas / Pascal Chappert / Jason Mercer / Juan Garcia-Arriaza / Olivier Schwartz / Pablo Guardado-Calvo /
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 ...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.
History
DepositionNov 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
C: Superinfection exclusion protein
D: Protein OPG185
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1718
Polymers137,0444
Non-polymers2,1274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Virion membrane protein OPG143


Mass: 39110.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG143, VACWR136, A16L / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P16710
#2: Protein Entry-fusion complex protein OPG094 / EFC protein OPG094 / Myristoylated protein G9 / Protein F1


Mass: 35601.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG094, VACWR087, G9R / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07611
#3: Protein Superinfection exclusion protein / Protein K2 / Serine proteinase inhibitor 3


Mass: 46738.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG040, K2L, SPI-3, VACWR033 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P18384
#4: Protein Protein OPG185 / Hemagglutinin


Mass: 15592.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG185, HA, VACWR181, A56R / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01218

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Sugars , 4 types, 4 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of K2
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.155 MDa / Experimental value: NO
Source (natural)Organism: Vaccinia virus / Strain: Western reserve
Source (recombinant)Organism: Drosophila melanogaster (fruit fly) / Cell: S2 cells
Buffer solutionpH: 7.5 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: concentration = 2 uM
Specimen supportGrid material: GOLD / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228433 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.28 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00298575
ELECTRON MICROSCOPYf_angle_d0.640311608
ELECTRON MICROSCOPYf_chiral_restr0.04511272
ELECTRON MICROSCOPYf_plane_restr0.00451481
ELECTRON MICROSCOPYf_dihedral_angle_d6.69321333

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