9K9R | pdb_00009k9r

MPXV DNA polymerase in complex with primer/5U template DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 213.9 kDa 
  • Atom Count: 14,230 
  • Modeled Residue Count: 1,681 
  • Deposited Residue Count: 1,738 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E4R218Monkeypox 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase processivity factor component A20426Monkeypox 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
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (25-MER)D [auth P]25Monkeypox virus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5U 38-MER)E [auth T]38Monkeypox virus
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 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)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