8WPF

Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exogenous DNA bearing one abasic site


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 insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.

Wang, X.Ma, L.Li, N.Gao, N.

(2023) Mol Cell 83: 4398

  • DOI: https://doi.org/10.1016/j.molcel.2023.10.038
  • Primary Citation of Related Structures:  
    8WPE, 8WPF, 8WPK, 8WPP

  • PubMed Abstract: 

    The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. However, the molecular roles of these viral factors remain unclear. Here, we characterize the structures of F8-A22-E4 and F8-A22-E4-H5 complexes in the presence of different primer-template DNA substrates. E4 is located upstream of F8 on the template single-stranded DNA (ssDNA) and is catalytically active, highlighting a functional coupling between DNA base-excision repair and DNA synthesis. Moreover, H5, in the form of tetramer, binds to the double-stranded DNA (dsDNA) region downstream of F8 in a similar position as PCNA (proliferating cell nuclear antigen) does in eukaryotic polymerase complexes. Omission of H5 or disruption of its DNA interaction showed a reduced synthesis of full-length DNA products. These structures provide snapshots for the working cycle of the polymerase and generate insights into the mechanisms of these essential factors in viral DNA replication.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase1,006Monkeypox virusMutation(s): 0 
UniProt
Find proteins for A0A7H0DN44 (Monkeypox virus)
Explore A0A7H0DN44 
Go to UniProtKB:  A0A7H0DN44
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UniProt GroupA0A7H0DN44
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
A22R DNA polymerase processivity factor437Monkeypox virusMutation(s): 0 
Gene Names: A22R
UniProt
Find proteins for A0A7H0DNC0 (Monkeypox virus)
Explore A0A7H0DNC0 
Go to UniProtKB:  A0A7H0DNC0
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UniProt GroupA0A7H0DNC0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E4R Uracil-DNA glycosylase, DNA polymerase processivity factor218Monkeypox virusMutation(s): 0 
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
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H5R late gene transcription factor
D, E, F, G
210Monkeypox virusMutation(s): 0 
UniProt
Find proteins for A0A7H0DN82 (Monkeypox virus)
Explore A0A7H0DN82 
Go to UniProtKB:  A0A7H0DN82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN82
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
Primer DNA35synthetic construct
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  • Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
Template DNA48synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3T
Query on D3T

Download Ideal Coordinates CCD File 
J [auth A]2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Database references