2DF7

Crystal structure of infectious bursal disease virus VP2 subviral particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of infectious bursal disease virus VP2 subviral particle at 2.6A resolution: Implications in virion assembly and immunogenicity.

Lee, C.C.Ko, T.P.Chou, C.C.Yoshimura, M.Doong, S.R.Wang, M.Y.Wang, A.H.

(2006) J Struct Biol 155: 74-86

  • DOI: 10.1016/j.jsb.2006.02.014
  • Primary Citation of Related Structures:  
    2DF7

  • PubMed Abstract: 
  • The structural protein VP2 of infectious bursal disease virus (IBDV) spontaneously forms a dodecahedral T=1 subviral particle (SVP), and is a primary immunogen of the virus. In this study, the structure of IBDV SVP was determined in a cubic crystal a ...

    The structural protein VP2 of infectious bursal disease virus (IBDV) spontaneously forms a dodecahedral T=1 subviral particle (SVP), and is a primary immunogen of the virus. In this study, the structure of IBDV SVP was determined in a cubic crystal and refined to 2.6A resolution. It contains 20 independent VP2 subunits in a crystallographic asymmetric unit. Each subunit is folded mainly into a shell domain and a protrusion domain, both with the Swiss-roll topology, plus a small helical base domain. Three VP2 subunits constitute a tight trimer, which is the building block of IBDV (sub)viral particles. The structure revealed a calcium ion bound to three pairs of symmetry-related Asp31 and Asp174 to stabilize the VP2 trimer. Our results of treatment of SVP with EGTA, a Ca(2+)-chelating reagent, indicated that the metal-ion may be important not only in maintaining highly stable quaternary structure but also in regulating the swelling and dissociation of the icosahedral particles. A Ca(2+)-dependent assembly pathway was thus proposed, which involves further interactions between the trimers. The 20 independent subunits showed conformational variations, with the surface loops of the protrusion domain being the most diverse. These loops are targets of the neutralizing antibodies. Several common interactions between the surface loops were clearly observed, suggesting a possible major conformation of the immunogenic epitopes.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray analysis of immunogenic virus-like particles formed by infectious bursal disease virus (IBDV) structural protein VP2
      Lee, C.C., Ko, T.P., Lee, M.S., Chou, C.C., Lai, S.Y., Wang, A.H.J., Wang, M.Y.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1234

    Organizational Affiliation

    Structural Biology Program, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan, ROC.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
structural polyprotein VP2ABCDEFGHIJKLMNOPQRST458Infectious bursal disease virusMutation(s): 3 
EC: 3.4.21
Find proteins for Q9WR38 (Avian infectious bursal disease virus)
Explore Q9WR38 
Go to UniProtKB:  Q9WR38
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B, C, G, H, I, P, R
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, G, H, I, P, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 316.412α = 90
b = 316.412β = 90
c = 316.412γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance