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- PDB-9r09: Structure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 5.7 -

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Basic information

Entry
Database: PDB / ID: 9r09
TitleStructure of A16/G9 (vaccinia virus) in complex with VHH D07 at pH 5.7
Components
  • Entry-fusion complex protein OPG094
  • VHH D07
  • 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 / DNA-templated transcription termination / helicase activity / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / DNA binding / ATP binding / membrane
Similarity search - Function
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
Similarity search - Domain/homology
Entry-fusion complex protein OPG094 / Virion membrane protein OPG143
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation
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

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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
J000: VHH D07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9038
Polymers95,3393
Non-polymers5645
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-28 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.558, 147.066, 183.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Virion membrane protein OPG143


Mass: 40941.340 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: 37432.238 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

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Antibody , 1 types, 1 molecules J000

#3: Antibody VHH D07


Mass: 16965.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 3 types, 219 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 5.7, 12 % PEG 20K w/v (cryoprotected in 33% glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564977646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564977646 Å / Relative weight: 1
ReflectionResolution: 2.45→39.94 Å / Num. obs: 47379 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.52 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 2.45→2.54 Å / Num. unique obs: 4516 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→39.34 Å / SU ML: 0.2812 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 2488 5.26 %
Rwork0.2168 44809 -
obs0.2187 47297 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.43 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 36 214 5701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225618
X-RAY DIFFRACTIONf_angle_d0.49287589
X-RAY DIFFRACTIONf_chiral_restr0.0403783
X-RAY DIFFRACTIONf_plane_restr0.0036989
X-RAY DIFFRACTIONf_dihedral_angle_d16.75672106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.50.31921190.26242397X-RAY DIFFRACTION100
2.5-2.550.34711240.27022465X-RAY DIFFRACTION100
2.55-2.60.28051410.25852479X-RAY DIFFRACTION99.89
2.6-2.660.29091160.25672436X-RAY DIFFRACTION100
2.66-2.730.35911290.3062494X-RAY DIFFRACTION100
2.73-2.80.35271510.28782412X-RAY DIFFRACTION100
2.8-2.890.29511380.26942471X-RAY DIFFRACTION100
2.89-2.980.29131260.25062464X-RAY DIFFRACTION99.96
2.98-3.090.28181240.24282503X-RAY DIFFRACTION100
3.09-3.210.29051630.24962435X-RAY DIFFRACTION100
3.21-3.360.27961380.2582488X-RAY DIFFRACTION100
3.36-3.530.29261490.24382459X-RAY DIFFRACTION100
3.53-3.750.25941290.21452494X-RAY DIFFRACTION99.96
3.75-4.040.24061500.20062493X-RAY DIFFRACTION100
4.04-4.450.2391420.18932513X-RAY DIFFRACTION100
4.45-5.090.18571420.17632553X-RAY DIFFRACTION100
5.09-6.410.22451620.19762536X-RAY DIFFRACTION100
6.41-39.340.19751450.17342717X-RAY DIFFRACTION99.83

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