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- EMDB-53936: Structure of A16/G9 in complex with A56/K2 at pH 5.5 (vaccinia virus) -

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Basic information

Entry
Database: EMDB / ID: EMD-53936
TitleStructure of A16/G9 in complex with A56/K2 at pH 5.5 (vaccinia virus)
Map data
Sample
  • Complex: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of A56
    • Protein or peptide: Virion membrane protein OPG143
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Superinfection exclusion protein
    • Protein or peptide: Protein OPG185
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspoxvirus / viral fusion / vaccinia virus / mpox virus / VIRAL PROTEIN
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 / Vaccinia virus Western Reserve
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsVernuccio R / Battini L / Meola A / Guardado-Calvo P
Funding support France, 1 items
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
DepositionJun 2, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53936.png

Downloads & links

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Map

FileDownload / File: emd_53936.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 208 pix.
= 237.12 Å		1.14 Å/pix.
x 208 pix.
= 237.12 Å		1.14 Å/pix.
x 208 pix.
= 237.12 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.16246091 - 0.2719634
Average (Standard dev.)0.00005377265 (±0.009978399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 237.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map after DEEPEMHANCER

Fileemd_53936_additional_1.map
AnnotationSharpened map after DEEPEMHANCER
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Additional map: Sharpened map after refinement

Fileemd_53936_additional_2.map
AnnotationSharpened map after refinement
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Half map: #1

Fileemd_53936_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_53936_half_map_2.map
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Sample components

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Entire : Quaternary complex of vaccinia virus A16, G9, K2, and the Ig doma...

EntireName: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of A56
Components
  • Complex: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of A56
    • Protein or peptide: Virion membrane protein OPG143
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Superinfection exclusion protein
    • Protein or peptide: Protein OPG185
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig doma...

SupramoleculeName: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of A56
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Vaccinia virus / Strain: Western reserve
Molecular weightTheoretical: 155 KDa

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Macromolecule #1: Virion membrane protein OPG143

MacromoleculeName: Virion membrane protein OPG143 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus Western Reserve
Molecular weightTheoretical: 39.110977 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: RSAAAVTLNR IKIAPGIADI RDKYMELGFN YPEYNRAVKF AEESYTYYYE TSPGEIKPKF CLIDGMSIDH CSSFIVPEFA KQYVLIHGE PCSSFKFRPG SLIYYQNEVT PEYIKDLKHA TDYIASGQRC HFIKKDYLLG DSDSVAKCCS KTNTKHCPKI F NNNYKTEH ...String:
RSAAAVTLNR IKIAPGIADI RDKYMELGFN YPEYNRAVKF AEESYTYYYE TSPGEIKPKF CLIDGMSIDH CSSFIVPEFA KQYVLIHGE PCSSFKFRPG SLIYYQNEVT PEYIKDLKHA TDYIASGQRC HFIKKDYLLG DSDSVAKCCS KTNTKHCPKI F NNNYKTEH CDDFMTGFCR NDPGNPNCLE WLRAKRKPAM STYSDICSKH MDARYCSEFI RIIRPDYFTF GDTALYVFCN DH KGNRNCW CANYPKSNSG DKYLGPRVCW LHECTDESRD RKWLYYNQDV QRTRCKYVGG SGLVPRGSGG SGGSHHHHHH HHG GSGTGG LNDIFEAQKI EWHE

UniProtKB: Virion membrane protein OPG143

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Macromolecule #2: Entry-fusion complex protein OPG094

MacromoleculeName: Entry-fusion complex protein OPG094 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus Western Reserve
Molecular weightTheoretical: 35.601871 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: AGGVSVELPK RDPPPGVPTD EMLLNVDKMH DVIAPAKLLE YVHIGPLAKD KEDKVKKRYP EFRLVNTGPG GLSALLRQSY AGTAPNCCR TFQRTHYWKK DGKISDKYEE GAVLESCWPD VHDTGKCDVD LFDWCQGDTF DRNICHQWIG SAFNRADRTV E GQQSLINL ...String:
AGGVSVELPK RDPPPGVPTD EMLLNVDKMH DVIAPAKLLE YVHIGPLAKD KEDKVKKRYP EFRLVNTGPG GLSALLRQSY AGTAPNCCR TFQRTHYWKK DGKISDKYEE GAVLESCWPD VHDTGKCDVD LFDWCQGDTF DRNICHQWIG SAFNRADRTV E GQQSLINL YNKMQTLCSK DASVPICESF LHHLRAHNTE DSKEMIDYIL RQQSADFKQK YMRCSYPTRD KLEESLKYAE PR ECWDPEC SNANVNFLLT RNYNNLGLCN IVRGSGLVPR GSLEDDDDKA GWSHPQFEKG GGSGGGSGGG SWSHPQFEK

UniProtKB: Entry-fusion complex protein OPG094

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Macromolecule #3: Superinfection exclusion protein

MacromoleculeName: Superinfection exclusion protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus Western Reserve
Molecular weightTheoretical: 46.73891 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: YRLQGFTNAG IVAYKNIQDD NIVFSPFGYS FSMFMSLLPA SGNTRIELLK TMDLRKRDLG PAFTELISGL AKLKTSKYTY TDLTYQSFV DNTVSIKPSY YQQYHRFGLY RLNFRRDAVN KINSIVERRS GMSNVVDSNM LDNNTLWAII NTIYFKGIWQ Y PFDITKTR ...String:
YRLQGFTNAG IVAYKNIQDD NIVFSPFGYS FSMFMSLLPA SGNTRIELLK TMDLRKRDLG PAFTELISGL AKLKTSKYTY TDLTYQSFV DNTVSIKPSY YQQYHRFGLY RLNFRRDAVN KINSIVERRS GMSNVVDSNM LDNNTLWAII NTIYFKGIWQ Y PFDITKTR NASFTNKYGT KTVPMMNVVT KLQGNTITID DEEYDMVRLP YKDANISMYL AIGDNMTHFT DSITAAKLDY WS FQLGNKV YNLKLPKFSI ENKRDIKSIA EMMAPSMFNP DNASFKHMTR DPLYIYKMFQ NAKIDVDEQG TVAEASTIMV ATA RSSPEK LEFNTPFVFI IRHDITGFIL FMGKVESPGS GLVPRGSGSA GWSHPQFEKG GGSGGGSGGG SWSHPQFEKG TGGL NDIFE AQKIEWHE

UniProtKB: Superinfection exclusion protein

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Macromolecule #4: Protein OPG185

MacromoleculeName: Protein OPG185 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus Western Reserve
Molecular weightTheoretical: 15.592021 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
RSTPFPQTSK KIGDDATLSC NRNNTNDYVV MSAWYKEPNS IILLAAKSDV LYFDNYTKDK ISYDSPYDDL VTTITIKSLT ARDAGTYVC AFFMTSTTND TDKVDYEEYS TELIVNTDSE GSGLVPRGSG SGHHHHHHHH

UniProtKB: Protein OPG185

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5 / Details: Tris 100 mM MES 50 mM NaOAc 50 mM NaCl 150 mM
GridModel: Quantifoil / Material: GOLD
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Detailsconcentration = 2 uM

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 205000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9hbk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65223
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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