9WGB | pdb_00009wgb

Cryo-EM structure of I3L-ssDNA double-ring complex

• PDB DOI: https://doi.org/10.2210/pdb9WGB/pdb
• EM Map EMD-65952: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Monkeypox virus Zaire-96-I-16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-23 Released: 2026-06-17 
• Deposition Author(s): Ma, J., Yang, K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Double-ring assembly of mpox virus I3L reveals an unconventional mechanism for ssDNA engagement.

Yang, K., Ge, M., Song, J., Zou, J., Zhang, Y., Wu, H., Wang, Y., Ma, J.

(2026) Cell Rep 45: 117659-117659

• PubMed: 42418326 
• DOI: https://doi.org/10.1016/j.celrep.2026.117659
• Primary Citation Related Structures: 
  9WGB


• PubMed 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 (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.

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Organizational Affiliation: 
• Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518132, China.
Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518132, China; College of Veterinary Medicine, Anhui Agricultural University, Hefei 230036, China.
College of Veterinary Medicine, Anhui Agricultural University, Hefei 230036, China. Electronic address: [e-mail].
Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518132, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 406.61 kDa 
• Atom Count: 25,888 
• Modeled Residue Count: 3,344 
• Deposited Residue Count: 3,648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein OPG079	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	228	Monkeypox virus Zaire-96-I-16	Mutation(s): 0  Gene Names: I3L
UniProt
Find proteins for Q8V516 (Monkeypox virus (strain Zaire-96-I-16)) Explore Q8V516  Go to UniProtKB:  Q8V516

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	RELION	4.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Ma, J., Yang, K.

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Funding Organization	Location	Grant Number
Other government	China	21330061

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release
  
• Version 2.0: 2026-08-19
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary