9L2R | pdb_00009l2r

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

• PDB DOI: https://doi.org/10.2210/pdb9L2R/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Penaeus monodon
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-17 Released: 2025-10-22 
• Deposition Author(s): Laohawutthichai, P., Kim, S.-Y., Chek, M.F., Krusong, K., Hakoshima, T.
• Funding Organization(s): Other government

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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) 

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

• PubMed: 40639753 
• DOI: https://doi.org/10.1016/j.jmb.2025.169329
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 21.96 kDa 
• Atom Count: 1,630 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral responsive protein	A, B, C	63	Penaeus monodon	Mutation(s): 0  Gene Names: VRP15
UniProt
Find proteins for X2FU51 (Penaeus monodon) Explore X2FU51  Go to UniProtKB:  X2FU51

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 66.619	α = 90
b = 115.297	β = 90
c = 54.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Laohawutthichai, P., Kim, S.-Y., Chek, M.F., Krusong, K., Hakoshima, T.

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Funding Organization	Location	Grant Number
Other government		N42A650259
Other government		21K15028

Revision History  

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