8XMS

Crystal structure of Porcine Circovirus type II Rep ATPase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of the ATPase domain of porcine circovirus type 2 Rep protein.

Guan, S.Li, Z.Han, Y.Tian, A.Zhou, S.Chen, H.Peng, G.Song, Y.

(2024) J Gen Virol 105

  • DOI: https://doi.org/10.1099/jgv.0.001972
  • Primary Citation of Related Structures:  
    8XMS

  • PubMed Abstract: 

    PCV2 belongs to the genus Circovirus in the family Circoviridae , whose genome is replicated by rolling circle replication (RCR). PCV2 Rep is a multifunctional enzyme that performs essential functions at multiple stages of viral replication. Rep is responsible for nicking and ligating single-stranded DNA and unwinding double-stranded DNA (dsDNA). However, the structure and function of the Rep are still poorly understood, which significantly impedes viral replication research. This study successfully resolved the structure of the PCV2 Rep ATPase domain (PRAD) using X-ray crystallography. Homologous structure search revealed that Rep belonged to the superfamily 3 (SF3) helicase, and multiple conserved residues were identified during sequence alignment with SF3 family members. Simultaneously, a hexameric PRAD model was generated for analysing characteristic structures and sites. Mutation of the conserved site and measurement of its activity showed that the hallmark motifs of the SF3 family influenced helicase activity by affecting ATPase activity and β-hairpin just caused the loss of helicase activity. The structural and functional analyses of the PRAD provide valuable insights for future research on PCV2 replication and antiviral strategies.


  • Organizational Affiliation

    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication-associated protein
A, B, C, D, E
A, B, C, D, E, F
163Porcine circovirus 2Mutation(s): 0 
Gene Names: RepORF1
EC: 2.7.7 (PDB Primary Data), 3.1.21 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt
Find proteins for Q8BB16 (Porcine circovirus 2)
Explore Q8BB16 
Go to UniProtKB:  Q8BB16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BB16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.92α = 90
b = 103.93β = 109.9
c = 76.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31972658

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release