8WGZ | pdb_00008wgz

MPOX E5 double hexamer ssDNA bound conformation

• PDB DOI: https://doi.org/10.2210/pdb8WGZ/pdb
• EM Map EMD-37523: EMDB EMDataResource
• NAKB: 8WGZ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Monkeypox virus, Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-09-22 Released: 2024-10-16 
• Deposition Author(s): Zhang, Z., Dong, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer.

Xu, Y., Wu, Y., Zhang, Y., Gao, K., Wu, X., Yang, Y., Li, D., Yang, B., Zhang, Z., Dong, C.

(2024) Sci Adv 10: eadl1150-eadl1150

• PubMed: 39167653 
• DOI: https://doi.org/10.1126/sciadv.adl1150
• Primary Citation of Related Structures:  
  8WGY, 8WGZ, 8WH0, 8WH2, 8WH3, 8WH4, 8WH6


• PubMed Abstract: 
  

  An outbreak of mpox virus in May 2022 has spread over 110 nonpandemic regions in the world, posing a great threat to global health. Mpox virus E5, a helicase-primase, plays an essential role in DNA replication, but the molecular mechanisms are elusive. Here, we report seven structures of mpox virus E5 in a double hexamer (DH) and six in single hexamer in different conformations, indicating a rotation mechanism for helicase and a coupling action for primase. The DH is formed through the interface of zinc-binding domains, and the central channel density indicates potential double-stranded DNA (dsDNA), which helps to identify dsDNA binding residues Arg ²⁴⁹ , Lys ²⁸⁶ , Lys ³¹⁵ , and Lys ³¹⁷ . Our work is important not only for understanding poxviral DNA replication but also for the development of novel therapeutics for serious poxviral infections including smallpox virus and mpox virus.

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Organizational Affiliation: 
• Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
The Cryo-EM Center, Core facility of Wuhan University, Wuhan University, Wuhan 430071, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,087.12 kDa 
• Atom Count: 51,396 
• Modeled Residue Count: 6,605 
• Deposited Residue Count: 9,425 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncoating factor OPG117	A, B, C, D, E, F, G, H, I, J, K, L	785	Monkeypox virus	Mutation(s): 0  Gene Names: E5R EC: 3.6.4
UniProt
Find proteins for A0A7H0DN89 (Monkeypox virus) Explore A0A7H0DN89  Go to UniProtKB:  A0A7H0DN89

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*CP*CP*C)-3')	M [auth T]	5	Spodoptera frugiperda

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Zhang, Z., Dong, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371303

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection