3IDE

Structure of IPNV subviral particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an aquabirnavirus particle: insights into antigenic diversity and virulence determinism

Coulibaly, F.Chevalier, C.Delmas, B.Rey, F.A.

(2010) J.Virol. 84: 1792-1799

  • DOI: 10.1128/JVI.01536-09

  • PubMed Abstract: 
  • Infectious pancreatic necrosis virus (IPNV), a pathogen of salmon and trout, imposes a severe toll on the aquaculture and sea farming industries. IPNV belongs to the Aquabirnavirus genus in the Birnaviridae family of bisegmented double-stranded RNA v ...

    Infectious pancreatic necrosis virus (IPNV), a pathogen of salmon and trout, imposes a severe toll on the aquaculture and sea farming industries. IPNV belongs to the Aquabirnavirus genus in the Birnaviridae family of bisegmented double-stranded RNA viruses. The virions are nonenveloped with a T=13l icosahedral capsid made by the coat protein VP2, the three-dimensional (3D) organization of which is known in detail for the family prototype, the infectious bursal disease virus (IBDV) of poultry. A salient feature of the birnavirus architecture is the presence of 260 trimeric spikes formed by VP2, projecting radially from the capsid. The spikes carry the principal antigenic sites as well as virulence and cell adaptation determinants. We report here the 3.4-A resolution crystal structure of a subviral particle (SVP) of IPNV, containing 20 VP2 trimers organized with icosahedral symmetry. We show that, as expected, the SVPs have a very similar organization to the IBDV counterparts, with VP2 exhibiting the same overall 3D fold. However, the spikes are significantly different, displaying a more compact organization with tighter packing about the molecular 3-fold axis. Amino acids controlling virulence and cell culture adaptation cluster differently at the top of the spike, i.e., in a central bowl in IBDV and at the periphery in IPNV. In contrast, the spike base features an exposed groove, conserved across birnavirus genera, which contains an integrin-binding motif. Thus, in addition to revealing the viral antigenic determinants, the structure suggests that birnaviruses interact with different receptors for attachment and for cell internalization during entry.


    Organizational Affiliation

    CNRS/INRA UMR 2472/1157 and IFR 115, Laboratoire de Virologie Mol├ęculaire et Structurale, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
A, B, C, D, E
442Infectious pancreatic necrosis virus (strain Sp)Mutation(s): 0 
Find proteins for Q703G9 (Infectious pancreatic necrosis virus (strain Sp))
Go to UniProtKB:  Q703G9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, C, E
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.217 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 303.431α = 90.00
b = 303.431β = 90.00
c = 303.431γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
SOLVEphasing
RESOLVEphasing
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description