3IDE

Structure of IPNV subviral particle

Summary for 3IDE

• Entry DOI: 10.2210/pdb3ide/pdb
• Descriptor: Capsid protein VP2, COBALT (II) ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: jelly roll, beta sandwich, icosahedral particle, virion, virus like particle
• Biological source: Infectious pancreatic necrosis virus - (IPNV)
• Cellular location: Capsid protein VP2: Virion . Capsid protein VP3: Virion . Structural peptide 1: Virion . Structural peptide 2: Virion . Structural peptide 3: Virion : Q703G9
• Total number of polymer chains: 5
• Total formula weight: 243140.60

Authors

Coulibaly, F.,Chevalier, C.,Delmas, B.,Rey, F.A. (deposition date: 2009-07-21, release date: 2009-12-29, Last modification date: 2024-03-20)

Primary citation

Coulibaly, F.,Chevalier, C.,Delmas, B.,Rey, F.A.
Crystal structure of an aquabirnavirus particle: insights into antigenic diversity and virulence determinism
J.Virol., 84:1792-1799, 2010

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 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.

PubMed: 20007275
DOI: 10.1128/JVI.01536-09

Experimental method

X-RAY DIFFRACTION (3.35 Å)