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- EMDB-64647: Cryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC... -

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Basic information

Entry
Database: EMDB / ID: EMD-64647
TitleCryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
Map dataMain_map_sharppen
Sample
  • Complex: The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
    • Protein or peptide: Virion membrane protein OPG143
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Envelope protein OPG155
    • Protein or peptide: Protein OPG107
    • Protein or peptide: Entry-fusion complex protein OPG086
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Protein OPG104
    • Protein or peptide: Virion membrane protein OPG147
    • Protein or peptide: Entry-fusion complex protein OPG076
KeywordsVaccinia Virus / Entry-Fusion Complex (EFC) / cryo-EM / Single-particle reconstruction / VIRAL PROTEIN
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 / 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 protein OPG086 / Entry-fusion complex protein OPG094 / Envelope protein OPG155 / Virion membrane protein OPG147
Similarity search - Component
Biological speciesOrthopoxvirus vaccinia
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWang CH / Lin CSH / Chang W
Funding support Taiwan, 2 items
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, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64647.png

Downloads & links

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Map

FileDownload / File: emd_64647.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain_map_sharppen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 640 pix.
= 339.52 Å		0.53 Å/pix.
x 640 pix.
= 339.52 Å		0.53 Å/pix.
x 640 pix.
= 339.52 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5305 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.8717633 - 2.5424097
Average (Standard dev.)0.00023518513 (±0.03919966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 339.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Main map unsharppen

Fileemd_64647_additional_1.map
AnnotationMain_map_unsharppen
Projections & Slices
AxesZYX

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Half map: Half-map-A

Fileemd_64647_half_map_1.map
AnnotationHalf-map-A
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Half map: Half-map-B

Fileemd_64647_half_map_2.map
AnnotationHalf-map-B
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Sample components

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Entire : The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit

EntireName: The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
Components
  • Complex: The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
    • Protein or peptide: Virion membrane protein OPG143
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Envelope protein OPG155
    • Protein or peptide: Protein OPG107
    • Protein or peptide: Entry-fusion complex protein OPG086
    • Protein or peptide: Entry-fusion complex protein OPG094
    • Protein or peptide: Protein OPG104
    • Protein or peptide: Virion membrane protein OPG147
    • Protein or peptide: Entry-fusion complex protein OPG076

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Supramolecule #1: The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit

SupramoleculeName: The Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Orthopoxvirus vaccinia

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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: Orthopoxvirus vaccinia
Molecular weightTheoretical: 43.48659 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAAVTLNRI KIAPGIADIR DKYMELGFNY PEYNRAVKFA EESYTYYYET SPGEIKPKFC LIDGMSIDHC SSFIVPEFAK QYVLIHGEP CSSFKFRPGS LIYYQNEVTP EYIKDLKHAT DYIASGQRCH FIKKDYLLGD SDSVAKCCSK TNTKHCPKIF N NNYKTEHC ...String:
MGAAVTLNRI KIAPGIADIR DKYMELGFNY PEYNRAVKFA EESYTYYYET SPGEIKPKFC LIDGMSIDHC SSFIVPEFAK QYVLIHGEP CSSFKFRPGS LIYYQNEVTP EYIKDLKHAT DYIASGQRCH FIKKDYLLGD SDSVAKCCSK TNTKHCPKIF N NNYKTEHC DDFMTGFCRN DPGNPNCLEW LRAKRKPAMS TYSDICSKHM DARYCSEFIR IIRPDYFTFG DTALYVFCND HK GNRNCWC ANYPKSNSGD KYLGPRVCWL HECTDESRDR KWLYYNQDVQ RTRCKYVGCT INVNSLALKN SQAELTSNCT RTT SAVGDV HPGEPVVKDK IKLPTWLGAA ITLVVISVIF YFISIYSRPK IKTNDINVRR R

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: Orthopoxvirus vaccinia
Molecular weightTheoretical: 38.840285 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGGVSVELP KRDPPPGVPT DEMLLNVDKM HDVIAPAKLL EYVHIGPLAK DKEDKVKKRY PEFRLVNTGP GGLSALLRQS YNGTAPNCC RTFNRTHYWK KDGKISDKYE EGAVLESCWP DVHDTGKCDV DLFDWCQGDT FDRNICHQWI GSAFNRSNRT V EGQQSLIN ...String:
MGGGVSVELP KRDPPPGVPT DEMLLNVDKM HDVIAPAKLL EYVHIGPLAK DKEDKVKKRY PEFRLVNTGP GGLSALLRQS YNGTAPNCC RTFNRTHYWK KDGKISDKYE EGAVLESCWP DVHDTGKCDV DLFDWCQGDT FDRNICHQWI GSAFNRSNRT V EGQQSLIN LYNKMQTLCS KDASVPICES FLHHLRAHNT EDSKEMIDYI LRQQSADFKQ KYMRCSYPTR DKLEESLKYA EP RECWDPE CSNANVNFLL TRNYNNLGLC NIVRCNTSVN NLQMDKTSSL RLSCGLSNSD RFSTVPVNRA KVVQHNIKHS FDL KLHLIS LLSLLVIWIL IVAI

UniProtKB: Entry-fusion complex protein OPG094

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Macromolecule #3: Envelope protein OPG155

MacromoleculeName: Envelope protein OPG155 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 16.340536 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MNSLSIFFIV VATAAVCLLF IQGYSIYENY GNIKEFNATH AAFEYSKSIG GTPALDRRVQ DVNDTISDVK QKWRCVVYPG NGFVSASIF GFQAEVGPNN TRSIRKFNTM QQCIDFTFSD VININIYNPC VVPNINNAEC QFLKSVL

UniProtKB: Envelope protein OPG155

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Macromolecule #4: Protein OPG107

MacromoleculeName: Protein OPG107 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 21.568877 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDKTTLSVNA CNLEYVREKA IVGVQAAKTS TLIFFVIILA ISALLLWFQT SDNPVFNELT RYMRIKNTVN DWKSLTDSKT KLESDRGRL LAAGKDDIFE FKCVDFGAYF IAMRLDKKTY LPQAIRRGTG DAWMVKKAAK VDPSAQQFCQ YLIKHKSNNV I TCGNEMLN ELGYSGYFMS PHWCSDFSNM E

UniProtKB: Protein OPG107

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Macromolecule #5: Entry-fusion complex protein OPG086

MacromoleculeName: Entry-fusion complex protein OPG086 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 12.814793 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASLLYLILF LLFVCISYYF TYYPTNKLQA AVMETDRENA IIRQRNDEIP TRTLDTAIFT DASTVASAQI HLYYNSNIGK IIMSLNGKK HTFNLYDDND IRTLLPILLL SK

UniProtKB: Entry-fusion complex protein OPG086

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Macromolecule #6: Entry-fusion complex protein OPG094

MacromoleculeName: Entry-fusion complex protein OPG094 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 15.062823 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MENVPNVYFN PVFIEPTFKH SLLSVYKHRL IVLFEVFVVF ILIYVFFRSE LNMFFMPKRK IPDPIDRLRR ANLACEDDKL MIYGLPWMT TQTSALSINS KPIVYKDCAK LLRSINGSQP VSLNDVLRR

UniProtKB: Entry-fusion complex protein OPG094

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Macromolecule #7: Protein OPG104

MacromoleculeName: Protein OPG104 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 15.174698 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MTDEQIYAFC DANKDDIRCK CIYPDKSIVR IGIDTRLPYY CWYEPCKRSD ALLPASLKKN ITKCNVSDCT ISLGNVSITD SKLDVNNVC DSKRVATENI AVRYLNQEIR YPIIDIKWLP IGLLALAILI LAFF

UniProtKB: Protein OPG104

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Macromolecule #8: Virion membrane protein OPG147

MacromoleculeName: Virion membrane protein OPG147 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 13.661822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MITLFLILCY FILIFNIIVP AISEKMRRER AAYVNYKRLN KNFICVDDRL FSYNFTTSGI KAKVAVDNKN VPIPCSKINE VNNNKDVDT LYCDKDRDDI PGFARSCYRA YSDLFFTT

UniProtKB: Virion membrane protein OPG147

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Macromolecule #9: Entry-fusion complex protein OPG076

MacromoleculeName: Entry-fusion complex protein OPG076 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 4.230069 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MLVVIMFFIA FAFCSWLSYS YLRPYISTKE LNKSR

UniProtKB: Entry-fusion complex protein OPG076

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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: 7.2 / Details: 2.5 mM biotin, 0.02% NP-40 in PBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.99 µm / Nominal defocus min: 0.13 µm
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 474787
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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