9K9V | pdb_00009k9v

MPXV DNA polymerase complex in editing state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of DNA replication fidelity of the Mpox virus.

Xie, Y.Kuai, L.Peng, Q.Wang, Q.Wang, H.Li, X.Qi, J.Ding, Q.Shi, Y.Gao, G.F.

(2025) Proc Natl Acad Sci U S A 122: e2411686122-e2411686122

  • DOI: https://doi.org/10.1073/pnas.2411686122
  • Primary Citation of Related Structures:  
    9K9R, 9K9S, 9K9T, 9K9U, 9K9V

  • PubMed Abstract: 

    The Mpox virus (MPXV) is an orthopoxvirus that caused a global outbreak in 2022. The poxvirus DNA polymerase complex is responsible for the replication and integrity of the viral genome; however, the molecular mechanisms underlying DNA replication fidelity are still unclear. In this study, we determined the cryoelectron microscopy (cryo-EM) structures of the MPXV F8-A22-E4 polymerase holoenzyme in its editing state, in complex with mismatched primer-template DNA and DNA containing uracil deoxynucleotide. We showed that the MPXV polymerase has a similar replication-to-edit transition mechanism to proofread the mismatched nucleotides like the B-family DNA polymerases of other species. The unique processivity cofactor A22-E4 undergoes conformational changes in different working states and might affect the proofreading process. Moreover, we elucidated the base excision repair (BER) function of E4 as a uracil-DNA glycosylase and the coupling mechanism of genome replication and BER, characteristic of poxviruses. Our findings greatly enhance our molecular understanding of DNA replication fidelity of orthopoxviruses and will stimulate the development of broad-spectrum antiviral drugs.


  • Organizational Affiliation
    • Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase1,031Monkeypox virusMutation(s): 2 
Gene Names: OPG071POLMPXVgp056
EC: 2.7.7.7
UniProt
Find proteins for A0A7H0DN44 (Monkeypox virus)
Explore A0A7H0DN44 
Go to UniProtKB:  A0A7H0DN44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN44
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil-DNA glycosylase218Monkeypox virusMutation(s): 0 
Gene Names: 
EC: 3.2.2.27
UniProt
Find proteins for M1LL92 (Monkeypox virus)
Explore M1LL92 
Go to UniProtKB:  M1LL92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1LL92
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase processivity factor426Monkeypox virusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A7H0DNC0 (Monkeypox virus)
Explore A0A7H0DNC0 
Go to UniProtKB:  A0A7H0DNC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DNC0
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (25-MER)D [auth P]25Monkeypox virus
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (38-MER)38Monkeypox virus
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection
  • Version 1.2: 2025-09-10
    Changes: Data collection, Database references