[English] 日本語
Yorodumi
- EMDB-52019: Structure of A16/G9 in complex with A56/K2 (vaccinia virus) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52019
TitleStructure of A16/G9 in complex with A56/K2 (vaccinia virus)
Map data
Sample
  • Complex: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of K2
    • 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 / helicase activity / DNA-templated transcription termination / 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 / helicase activity / DNA-templated transcription termination / 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: 3.2 Å
AuthorsVernuccio R / 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
DepositionNov 7, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52019.png

Downloads & links

-
Map

FileDownload / File: emd_52019.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 180 pix.
= 232.2 Å		1.29 Å/pix.
x 180 pix.
= 232.2 Å		1.29 Å/pix.
x 180 pix.
= 232.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.28315163 - 0.56522053
Average (Standard dev.)0.00013642003 (±0.018961998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 232.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52019_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 K2
Components
  • Complex: Quaternary complex of vaccinia virus A16, G9, K2, and the Ig domain of K2
    • 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

-
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 K2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Vaccinia virus / Strain: Western reserve
Molecular weightTheoretical: 155 KDa

-
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

-
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

-
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

-
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

-
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: PBS
GridModel: Quantifoil / Material: GOLD
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Detailsconcentration = 2 uM

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228433
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more