1W8X

Structural analysis of PRD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights Into Assembly from Structural Analysis of Bacteriophage Prd1.

Abrescia, N.G.A.Cockburn, J.J.B.Grimes, J.M.Sutton, G.C.Diprose, J.M.Butcher, S.J.Fuller, S.D.San Martin, C.Burnett, R.M.Stuart, D.I.Bamford, D.H.Bamford, J.K.H.

(2004) Nature 432: 68

  • DOI: 10.1038/nature03056

  • PubMed Abstract: 
  • The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have ...

    The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.


    Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR CAPSID PROTEIN (PROTEIN P3)
A, B, C, D, E, F, G, H, I, J, K, L
395Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: III
Find proteins for P22535 (Enterobacteria phage PRD1)
Go to UniProtKB:  P22535
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN P30
M
83Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: XXX (P)
Find proteins for P27391 (Enterobacteria phage PRD1)
Go to UniProtKB:  P27391
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN P31
N
126Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: XXXI (C)
Find proteins for P27384 (Enterobacteria phage PRD1)
Go to UniProtKB:  P27384
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN P16
P
117Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: XVI (S)
Find proteins for P27392 (Enterobacteria phage PRD1)
Go to UniProtKB:  P27392
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 903.000α = 90.00
b = 920.600β = 90.00
c = 926.200γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-11
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references, Derived calculations, Other, Version format compliance