9L2R | pdb_00009l2r

Crystal structure of the SeMet-derived C-terminal of viral responsive protein 15 (PmVRP15) from black tiger shrimp Penaeus monodon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the C-terminal of Viral Responsive Protein 15 (VRP15): A Key Protein During White Spot Syndrome Virus (WSSV) Infection.

Laohawutthichai, P.Kim, S.Y.Chek, M.F.Jatuyosporn, T.Tassanakajon, A.Krusong, K.Hakoshima, T.

(2025) J Mol Biology 437: 169329-169329

  • DOI: https://doi.org/10.1016/j.jmb.2025.169329
  • Primary Citation of Related Structures:  
    9L2R, 9L2W

  • PubMed Abstract: 

    White spot syndrome virus (WSSV) is a major serious threat to black tiger shrimp farming. WSSV infection induces a host protein, viral responsive protein 15 (VRP15), for viral assembly and nuclear egress. Here, we showed that the C-terminal tail of VRP15 (VRP15-C) interacts directly with the viral nucleocapsid tegument protein WSV399. The crystal structure of VRP15-C was determined at 1.5 Å. The structure showed that VRP15-C forms a dimer by forming an α-helix bundle structure and that the dimer further interacts with adjacent dimers to form a tetramer and a higher oligomer by intermolecular helix-helix interactions. The ability to form oligomeric forms may contribute to assembly of viral proteins to form a nucleocapsid of WSSV.


  • Organizational Affiliation
    • Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Structural Biology and Protein Engineering Laboratory, Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Viral responsive protein
A, B, C
63Penaeus monodonMutation(s): 0 
Gene Names: VRP15
UniProt
Find proteins for X2FU51 (Penaeus monodon)
Explore X2FU51 
Go to UniProtKB:  X2FU51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX2FU51
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.619α = 90
b = 115.297β = 90
c = 54.935γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentN42A650259
Other government21K15028

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release