8J86

Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex in a DNA binding form


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir.

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

(2024) Int J Biol Macromol 270: 132231-132231

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.132231
  • Primary Citation of Related Structures:  
    8J86, 8J8F, 8J8G

  • PubMed Abstract: 

    Mpox virus has wildly spread over 108 non-endemic regions in the world since May 2022. DNA replication of mpox is performed by DNA polymerase machinery F8-A22-E4, which is known as a great drug target. Brincidofovir and cidofovir are reported to have broad-spectrum antiviral activity against poxviruses, including mpox virus in animal models. However, the molecular mechanism is not understood. Here we report cryogenic electron microscopy structures of mpox viral F8-A22-E4 in complex with a DNA duplex, or dCTP and the DNA duplex, or cidofovir diphosphate and the DNA duplex at resolution of 3.22, 2.98 and 2.79 Å, respectively. Our structural work and DNA replication inhibition assays reveal that cidofovir diphosphate is located at the dCTP binding position with a different conformation to compete with dCTP to incorporate into the DNA and inhibit DNA synthesis. Conformation of both F8-A22-E4 and DNA is changed from the pre-dNTP binding state to DNA synthesizing state after dCTP or cidofovir diphosphate is bound, suggesting a coupling mechanism. This work provides the structural basis of DNA synthesis inhibition by brincidofovir and cidofovir, providing a rational strategy for new therapeutical development for mpox virus and other pox viruses.


  • Organizational Affiliation

    Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase1,029Monkeypox virusMutation(s): 2 
Gene Names: F8L
UniProt
Find proteins for Q5IXW8 (Monkeypox virus)
Explore Q5IXW8 
Go to UniProtKB:  Q5IXW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5IXW8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E4R241Monkeypox virusMutation(s): 0 
Gene Names: E4R
EC: 3.2.2.27
UniProt
Find proteins for Q5IXS4 (Monkeypox virus)
Explore Q5IXS4 
Go to UniProtKB:  Q5IXS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5IXS4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase processivity factor component A20426Monkeypox virusMutation(s): 0 
Gene Names: A22R
UniProt
Find proteins for Q5IXP2 (Monkeypox virus)
Explore Q5IXP2 
Go to UniProtKB:  Q5IXP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5IXP2
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*CP*TP*GP*CP*TP*AP*TP*GP*TP*GP*AP*GP*AP*TP*TP*AP*AP*GP*TP*TP*AP*T)-3')D [auth P]24DNA molecule
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*CP*TP*TP*AP*AP*TP*CP*TP*CP*AP*CP*AP*TP*AP*GP*CP*AP*GP*CP*TP*)-3')E [auth T]38DNA molecule
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32250710142

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references