3ZED

X-ray structure of the birnavirus VP1-VP3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.1 of the entry. See complete history


Literature

Structure of a Vp1-Vp3 Complex Suggests How Birnaviruses Package the Vp1 Polymerase.

Bahar, M.W.Sarin, L.P.Graham, S.C.Pang, J.Bamford, D.H.Stuart, D.I.Grimes, J.M.

(2013) J Virol 87: 3229

  • DOI: 10.1128/JVI.02939-12
  • Primary Citation of Related Structures:  
    3ZED

  • PubMed Abstract: 
  • Infectious pancreatic necrosis virus (IPNV), a member of the family Birnaviridae, infects young salmon, with a severe impact on the commercial sea farming industry. Of the five mature proteins encoded by the IPNV genome, the multifunctional VP3 has an essential role in morphogenesis; interacting with the capsid protein VP2, the viral double-stranded RNA (dsRNA) genome and the RNA-dependent RNA polymerase VP1 ...

    Infectious pancreatic necrosis virus (IPNV), a member of the family Birnaviridae, infects young salmon, with a severe impact on the commercial sea farming industry. Of the five mature proteins encoded by the IPNV genome, the multifunctional VP3 has an essential role in morphogenesis; interacting with the capsid protein VP2, the viral double-stranded RNA (dsRNA) genome and the RNA-dependent RNA polymerase VP1. Here we investigate one of these VP3 functions and present the crystal structure of the C-terminal 12 residues of VP3 bound to the VP1 polymerase. This interaction, visualized for the first time, reveals the precise molecular determinants used by VP3 to bind the polymerase. Competition binding studies confirm that this region of VP3 is necessary and sufficient for VP1 binding, while biochemical experiments show that VP3 attachment has no effect on polymerase activity. These results indicate how VP3 recruits the polymerase into birnavirus capsids during morphogenesis.


    Organizational Affiliation

    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEA, B, C853Infectious pancreatic necrosis virusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P22173 (Infectious pancreatic necrosis virus (strain Jasper))
Explore P22173 
Go to UniProtKB:  P22173
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CAPSID PROTEIN VP3D, E, F242Infectious pancreatic necrosis virusMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for P05844 (Infectious pancreatic necrosis virus (strain Jasper))
Explore P05844 
Go to UniProtKB:  P05844
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.27α = 90
b = 341.87β = 90
c = 59.7γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references