7C5Z | pdb_00007c5z

Crystal structure of spring viremia of carp virus phosphoprotein central domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

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Literature

Structural and Functional Characterization of the Phosphoprotein Central Domain of Spring Viremia of Carp Virus.

Wang, Z.X.Liu, S.B.Guan, H.Lu, L.F.Tu, J.G.Ouyang, S.Zhang, Y.A.

(2020) J Virol 94

  • DOI: https://doi.org/10.1128/JVI.00855-20
  • Primary Citation Related Structures: 
    7C5Z

  • PubMed Abstract: 

    Spring viremia of carp virus (SVCV) is a highly pathogenic Vesiculovirus in the common carp. The phosphoprotein (P protein) of SVCV is a multifunctional protein that acts as a polymerase cofactor and an antagonist of cellular interferon (IFN) response. Here, we report the 1.5-Å-resolution crystal structure of the P protein central domain (P CD ) of SVCV (SVCV PCD ). The P CD monomer consists of two β sheets, an α helix, and another two β sheets. Two P CD monomers pack together through their hydrophobic surfaces to form a dimer. The mutations of residues on the hydrophobic surfaces of P CD disrupt the dimer formation to different degrees and affect the expression of host IFN consistently. Therefore, the oligomeric state formation of the P protein of SVCV is an important mechanism to negatively regulate host IFN response. IMPORTANCE SVCV can cause spring viremia of carp with up to 90% lethality, and it is the homologous virus of the notorious vesicular stomatitis virus (VSV). There are currently no drugs that effectively cure this disease. P proteins of negative-strand RNA viruses (NSVs) play an essential role in many steps during the replication cycle and an additional role in immunosuppression as a cofactor. All P proteins of NSVs are oligomeric, but the studies on the role of this oligomerization mainly focus on the process of virus transcription or replication, and there are few studies on the role of P CD in immunosuppression. Here, we present the crystal structure of SVCV PCD A new mechanism of immune evasion is clarified by exploring the relationship between SVCV PCD and host IFN response from a structural biology point of view. These findings may provide more accurate target sites for drug design against SVCV and provide new insights into the function of NSV PCD .


  • Organizational Affiliation
    • State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 19.54 kDa 
  • Atom Count: 1,362 
  • Modeled Residue Count: 166 
  • Deposited Residue Count: 172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoprotein
A, B
86Sprivivirus cyprinusMutation(s): 0 
UniProt
Find proteins for A7J936 (Spring viremia of carp virus)
Explore A7J936 
Go to UniProtKB:  A7J936
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7J936
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.9α = 90
b = 54.11β = 90
c = 89.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)China31725026
National Science Foundation (NSF, United States)China31770948
National Science Foundation (NSF, United States)China31570875

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary