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- PDB-9uzp: Cryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC... -

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Basic information

Entry
Database: PDB / ID: 9uzp
TitleCryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC) Including the F9 Subunit
Components
  • (Entry-fusion complex protein ...) x 4
  • (Virion membrane protein ...) x 2
  • Entry-fusion complex associated protein OPG083
  • Envelope protein OPG155
  • Protein OPG104
  • Protein OPG107
KeywordsVIRAL PROTEIN / Vaccinia Virus / Entry-Fusion Complex (EFC) / cryo-EM / Single-particle reconstruction
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / DNA-templated transcription termination / helicase activity / hydrolase activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / DNA binding ...membrane fusion involved in viral entry into host cell / DNA-templated transcription termination / helicase activity / hydrolase activity / host cell endoplasmic reticulum membrane / 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
Poxvirus A21 / Poxvirus A21 Protein / Poxvirus L5 / Poxvirus G3 / Poxvirus L5 protein family / Chordopoxvirus G3 protein / Viral late protein H2 / Poxvirus A28 / Viral late protein H2 / Poxvirus A28 family ...Poxvirus A21 / Poxvirus A21 Protein / Poxvirus L5 / Poxvirus G3 / Poxvirus L5 protein family / Chordopoxvirus G3 protein / Viral late protein H2 / Poxvirus A28 / Viral late protein H2 / Poxvirus A28 family / Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
Similarity search - Domain/homology
Entry-fusion complex protein OPG094 / Protein OPG104 / Protein OPG107 / Entry-fusion complex protein OPG076 / Virion membrane protein OPG143 / Entry-fusion complex associated protein OPG083 / Entry-fusion complex protein OPG086 / Entry-fusion complex protein OPG094 / Envelope protein OPG155 / Virion membrane protein OPG147
Similarity search - Component
Biological speciesOrthopoxvirus vaccinia
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWang, C.H. / Lin, C.S.H. / Chang, W.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM structure of the vaccinia virus entry fusion complex reveals a multicomponent fusion machinery.
Authors: Chang Sheng-Huei Lin / Ching-An Li / Chun-Hsiung Wang / Chi-Fei Kao / Hsiao-Jung Chiu / Min-Chi Yeh / Hua-De Gao / Meng-Chiao Ho / Hsien-Ming Lee / Wen Chang
Abstract: Membrane fusion is essential for viral entry. Unlike class I-III fusion proteins, vaccinia virus (VACV) uses a multicomponent entry fusion complex (EFC). Using cryo-electron microscopy, we determined ...Membrane fusion is essential for viral entry. Unlike class I-III fusion proteins, vaccinia virus (VACV) uses a multicomponent entry fusion complex (EFC). Using cryo-electron microscopy, we determined the full-length structure of the VACV EFC at near-atomic resolution, revealing a 15-protein asymmetric assembly organized into three layers. The central A16/G9/J5 heterotrimer forms the fusion core, stabilized by conserved PXXCW and Delta motifs, and anchors two A28/H2 adaptor dimers linked to peripheral G3/L5/A21/O3 scaffolds. Structural and evolutionary analyses identify a conserved N-terminal domain in A16 containing a myristoyl-binding pocket and a phenylalanine-rich region that stabilizes the trimer and may regulate lipid engagement. An additional component, F9, binds peripherally to J5, A21, and H2 through Delta-like motifs, reinforcing the prefusion architecture. Together, these results define the VACV EFC as a unique multiprotein fusion machinery and provide a structural framework for understanding the mechanism of poxvirus entry and membrane fusion.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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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: Envelope protein OPG155
D: Protein OPG107
E: Entry-fusion complex protein OPG086
F: Entry-fusion complex protein OPG094
G: Entry-fusion complex associated protein OPG083
I: Protein OPG104
J: Virion membrane protein OPG147
K: Entry-fusion complex protein OPG076
c: Envelope protein OPG155
d: Protein OPG107
e: Entry-fusion complex protein OPG086
f: Entry-fusion complex protein OPG094
j: Virion membrane protein OPG147
k: Entry-fusion complex protein OPG076


Theoretical massNumber of molelcules
Total (without water)288,76016
Polymers288,76016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Virion membrane protein ... , 2 types, 3 molecules AJj

#1: Protein Virion membrane protein OPG143


Mass: 43486.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG143, VACWR136, A16L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P16710
#9: Protein Virion membrane protein OPG147


Mass: 13661.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG147, VACWR140, A21L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P68712

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Entry-fusion complex protein ... , 4 types, 7 molecules BEeFfKk

#2: Protein Entry-fusion complex protein OPG094 / EFC protein OPG094 / Myristoylated protein G9 / Protein F1


Mass: 38840.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG094, VACWR087, G9R / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P07611
#5: Protein Entry-fusion complex protein OPG086 / EFC protein OPG086


Mass: 12814.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG086, VACWR079, G3L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P68458
#6: Protein Entry-fusion complex protein OPG094 / EFC protein OPG094 / Protein F6 / Protein L5


Mass: 15062.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG099, VACWR092, L5R / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P68623
#10: Protein/peptide Entry-fusion complex protein OPG076 / EFC protein OPG076


Mass: 4230.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG076, VACWR069.5, O3L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P0CK21

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Protein , 4 types, 6 molecules CcDdGI

#3: Protein Envelope protein OPG155


Mass: 16340.536 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG155, VACWR151, A28L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P68633
#4: Protein Protein OPG107


Mass: 21568.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG107, VACWR100, H2R / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P08583
#7: Protein Entry-fusion complex associated protein OPG083 / EFC-associated protein OPG053 / Protein F9


Mass: 23900.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG053, VACWR048, F9L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P24361
#8: Protein Protein OPG104 / Protein F11 / Protein J5


Mass: 15174.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG104, VACWR097, J5L / Cell line (production host): Hela S3 cells / Production host: Homo sapiens (human) / References: UniProt: P07618

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Details

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: The Vaccinia Virus Entry/Fusion Complex (EFC) Including the F9 Subunit
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Orthopoxvirus vaccinia
Source (recombinant)Organism: Homo sapiens (human) / Cell: Hela S3 cells
Buffer solutionpH: 7.2 / Details: 2.5 mM biotin, 0.02% NP-40 in PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The Vaccinia Virus Entry/Fusion Complex (EFC) Including the F9 Subunit
VitrificationCryogen 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 defocus max: 4990 nm / Nominal defocus min: 130 nm
Image recordingElectron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 474787 / Symmetry type: POINT

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