1WCE | pdb_00001wce

Crystal structure of the T13 IBDV viral particle reveals a missing link in icosahedral viruses evolution

• PDB DOI: https://doi.org/10.2210/pdb1WCE/pdb

• Classification: VIRUS
• Organism(s): Infectious bursal disease virus
• Mutation(s): No 


• Deposited: 2004-11-12 Released: 2005-04-06 
• Deposition Author(s): Coulibaly, F., Chevalier, C., Gutsche, I., Pous, J., Bressanelli, S., Navaza, J., Delmas, B., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Work: 
  0.370 (DCC) 

Starting Model: experimental

Literature

The Birnavirus Crystal Structure Reveals Structural Relationships Among Icosahedral Viruses.

Coulibaly, F., Chevalier, C., Gutsche, I., Pous, J., Navaza, J., Bressanelli, S., Delmas, B., Rey, F.A.

(2005) Cell 120: 761

• PubMed: 15797378 
• DOI: https://doi.org/10.1016/j.cell.2005.01.009
• Primary Citation Related Structures: 
  1WCD, 1WCE


• PubMed Abstract: 
  

  Double-stranded RNA virions are transcriptionally competent icosahedral particles that must translocate across a lipid bilayer to function within the cytoplasm of the target cell. Birnaviruses are unique among dsRNA viruses as they have a single T = 13 icosahedral shell, lacking the characteristic inner capsid observed in the others. We determined the crystal structures of the T = 1 subviral particle (260 angstroms in diameter) and of the T = 13 intact virus particle (700 angstroms in diameter) of an avian birnavirus to 3 angstroms and 7 angstroms resolution, respectively. Our results show that VP2, the only component of the virus icosahedral capsid, is homologous both to the capsid protein of positive-strand RNA viruses, like the T = 3 nodaviruses, and to the T = 13 capsid protein of members of the Reoviridae family of dsRNA viruses. Together, these results provide important insights into the multiple functions of the birnavirus capsid and reveal unexpected structural relationships among icosahedral viruses.

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Organizational Affiliation: 
• Laboratoire de Virologie Moléculaire et Structurale, UMR 2472/1157 CNRS-INRA and IFR 115, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 780-mer - A780 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 613.86 kDa 
• Atom Count: 5,533 
• Modeled Residue Count: 5,533 
• Deposited Residue Count: 5,733 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR STRUCTURAL PROTEIN VP2	A, B, C, D, E, F, G, H, I, J, K, L, M	441	Infectious bursal disease virus	Mutation(s): 0
UniProt
Find proteins for P15480 (Avian infectious bursal disease virus (strain Cu-1)) Explore P15480  Go to UniProtKB:  P15480

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Work:  0.370 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 854.01	α = 90
b = 692.23	β = 90
c = 792.41	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
URO	phasing
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-06 
Deposition Author(s): Coulibaly, F., Chevalier, C., Gutsche, I., Pous, J., Bressanelli, S., Navaza, J., Delmas, B., Rey, F.A.

Revision History  

• Version 1.0: 2005-04-06
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description