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- PDB-9wgb: Cryo-EM structure of I3L-ssDNA double-ring complex -

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Basic information

Entry
Database: PDB / ID: 9wgb
TitleCryo-EM structure of I3L-ssDNA double-ring complex
ComponentsProtein OPG079
KeywordsVIRAL PROTEIN / ssDNA-binding / DNA replication / double-ring complex / OB-like
Function / homologyPoxvirus I3 ssDNA-binding / Poxvirus I3 ssDNA-binding protein / chromosome condensation / single-stranded DNA binding / host cell cytoplasm / Protein OPG079
Function and homology information
Biological speciesMonkeypox virus Zaire-96-I-16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMa, J. / Yang, K.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21330061 China
CitationJournal: Cell Rep / Year: 2026
Title: Double-ring assembly of mpox virus I3L reveals an unconventional mechanism for ssDNA engagement.
Authors: Kankan Yang / Mengrui Ge / Jinmiao Song / Junwei Zou / Yingying Zhang / Haiqiang Wu / Yong Wang / Jun Ma /
Abstract: Poxviruses, including variola and mpox virus (MPXV), are large dsDNA viruses that replicate their genomes in the host cytoplasm via virally encoded proteins. The single-stranded DNA-binding protein ...Poxviruses, including variola and mpox virus (MPXV), are large dsDNA viruses that replicate their genomes in the host cytoplasm via virally encoded proteins. The single-stranded DNA-binding protein (SSB) I3L is an essential component of this replication machinery, yet its structural mechanism remains to be fully elucidated. Here, we determined the cryo-EM structure of MPXV I3L and constructed a structural model of its complex with ssDNA. Unlike canonical SSBs, I3L forms an architectural double-ring assembly. The individual I3L protomer adopts an OB-fold variant with specialized elements beyond the classic pattern. Furthermore, biochemical assays and structural modeling suggest an assembly-dependent ssDNA-engagement mode, while monomeric binding features remain conserved. These distinctive structural features suggest a specialized molecular mechanism for poxviral DNA replication. Our findings advance the mechanistic understanding of poxvirus genome maintenance and provide perspectives for antiviral development against MPXV.
History
DepositionAug 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 2.0Aug 19, 2026Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
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Revision 1.1Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein OPG079
B: Protein OPG079
C: Protein OPG079
D: Protein OPG079
E: Protein OPG079
F: Protein OPG079
G: Protein OPG079
H: Protein OPG079
I: Protein OPG079
J: Protein OPG079
K: Protein OPG079
L: Protein OPG079
M: Protein OPG079
N: Protein OPG079
O: Protein OPG079
P: Protein OPG079


Theoretical massNumber of molelcules
Total (without water)406,60716
Polymers406,60716
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

#1: Protein
Protein OPG079 / ssDNA-bining protein I3L


Mass: 25412.959 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus Zaire-96-I-16 / Gene: I3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8V516
Has protein modificationN

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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: I3L double-ring complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus Zaire-96-I-16
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.1particle selection
9PHENIX1.20.1_4487model refinement
13RELION4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340355 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226176
ELECTRON MICROSCOPYf_angle_d0.5435232
ELECTRON MICROSCOPYf_dihedral_angle_d3.4243568
ELECTRON MICROSCOPYf_chiral_restr0.0454288
ELECTRON MICROSCOPYf_plane_restr0.0024336

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