9ILY | pdb_00009ily

The Cryo-EM structure of MPXV E5 in the apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Assembly and breakage of head-to-head double hexamer reveals mpox virus E5-catalyzed DNA unwinding initiation.

Cheng, Y.Han, P.Peng, Q.Liu, R.Liu, H.Yuan, B.Zhao, Y.Kuai, L.Qi, J.Miao, K.Shi, Y.Gao, G.F.Wang, H.

(2025) Nat Commun 16: 5176-5176

  • DOI: https://doi.org/10.1038/s41467-025-60539-1
  • Primary Citation Related Structures: 
    9ILY, 9ILZ, 9IM0, 9IM1, 9IM2, 9IM3

  • PubMed Abstract: 

    The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as fusion proteins in some organisms and viruses. However, the mechanism underlying DNA unwinding initiation by these helicase-primase fusion enzymes and the functional association between domains have not been elucidated. Herein, we report the cryo-EM structures of mpox virus E5, the founding member of these helicase-primase enzymes, in various enzymatic stages. Notably, E5 forms a head-to-head double hexamer encircling dsDNA, disrupted by the conformational rearrangement of primase domains upon nucleotide incorporation. Five E5-ssDNA-ATP structures further support an ATP cycle-driven non-classical escort model for E5 translocation. Finally, the helicase domain is found to enhance the primase function as a DNA scaffold. Together, our data shed light on the E5-mediated DNA unwinding model including dsDNA loading, DNA melting, ssDNA translocation, and provide a reasonable interpretation for evolutionary preservation of helicase-primase fusion from a functional perspective.


  • Organizational Affiliation
    • College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.

Macromolecule Content 

  • Total Structure Weight: 542.86 kDa 
  • Atom Count: 20,595 
  • Modeled Residue Count: 2,532 
  • Deposited Residue Count: 4,710 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Primase D5785Monkeypox virusMutation(s): 0 
Gene Names: 
EC: 3.6.4
UniProt
Find proteins for A0A7H0DN89 (Monkeypox virus)
Explore A0A7H0DN89 
Go to UniProtKB:  A0A7H0DN89
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN89
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32270157

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection