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- PDB-9hl2: Structure of A56/K2 (vaccinia virus) -

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Basic information

Entry
Database: PDB / ID: 9hl2
TitleStructure of A56/K2 (vaccinia virus)
Components
  • Protein OPG185
  • Superinfection exclusion protein
KeywordsVIRAL PROTEIN / poxvirus / viral fusion / vaccinia virus / mpox virus
Function / homology
Function and homology information


host cell membrane / serine-type endopeptidase inhibitor activity / viral envelope / host cell plasma membrane / virion membrane / extracellular space / membrane
Similarity search - Function
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 ...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
DI(HYDROXYETHYL)ETHER / Superinfection exclusion protein / Protein OPG185
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionDec 4, 2024Deposition 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: Superinfection exclusion protein
B: Protein OPG185
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6048
Polymers62,3312
Non-polymers1,2736
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint16 kcal/mol
Surface area21190 Å2
Unit cell
Length a, b, c (Å)74.372, 74.372, 216.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: 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
#2: 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 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01218

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 28 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na3 citrate, 0.1 M TRIS pH 8.5, 30% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980096 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980096 Å / Relative weight: 1
ReflectionResolution: 2.8→37.7 Å / Num. obs: 15779 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 67.11 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2233 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.7 Å / SU ML: 0.426 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2871 776 4.94 %
Rwork0.2333 14928 -
obs0.236 15704 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 84 24 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023985
X-RAY DIFFRACTIONf_angle_d0.52175391
X-RAY DIFFRACTIONf_chiral_restr0.0456613
X-RAY DIFFRACTIONf_plane_restr0.0035677
X-RAY DIFFRACTIONf_dihedral_angle_d11.99871535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.40391370.34922424X-RAY DIFFRACTION99.61
2.98-3.20.3881140.30632429X-RAY DIFFRACTION99.69
3.21-3.530.33441290.25652441X-RAY DIFFRACTION99.65
3.53-4.040.23691160.22712476X-RAY DIFFRACTION99.85
4.04-5.080.24381260.1882503X-RAY DIFFRACTION99.89
5.09-37.70.27891540.22442655X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.37879038706-0.633829371363-1.013540628712.277357196371.644063694884.073581458990.0139135830876-0.0815669406502-0.0627617725706-0.03109987781060.01514352805840.05982268265780.421405112618-0.0453564498543-4.16753263632E-60.720272582615-0.0667936391665-0.01445523989630.7305031759560.05550804219960.74040831271-23.91407580068.55814194741-11.0398311538
21.723749355140.326955090116-0.7123820943683.12601851114-0.542714747941.465525346020.0106254841051-0.08083355324680.122060555448-0.350589260738-0.104983067044-0.00257991498077-0.4239530677020.403609396825-1.5178085519E-51.01581015988-0.1539532396750.01679334722960.845799357874-0.01914328133130.850626030895-25.198314244739.3760502743-14.7357036039
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 360)AA1 - 3601 - 360
22(chain 'B' and resid 1 through 114)BH1 - 1141 - 114

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