3ZED

X-ray structure of the birnavirus VP1-VP3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


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

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-DIRECTED RNA POLYMERASE
A, B, C
853Infectious pancreatic necrosis virus (strain Jasper)Mutation(s): 0 
Gene Names: VP1
EC: 2.7.7.48
Find proteins for P22173 (Infectious pancreatic necrosis virus (strain Jasper))
Go to UniProtKB:  P22173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CAPSID PROTEIN VP3
D, E, F
242Infectious pancreatic necrosis virus (strain Jasper)Mutation(s): 0 
Find proteins for P05844 (Infectious pancreatic necrosis virus (strain Jasper))
Go to UniProtKB:  P05844
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.270α = 90.00
b = 341.870β = 90.00
c = 59.700γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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