1YQ5

PRD1 vertex protein P5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.

Merckel, M.C.Huiskonen, J.T.Bamford, D.H.Goldman, A.Tuma, R.

(2005) Mol Cell 18: 161-170

  • DOI: https://doi.org/10.1016/j.molcel.2005.03.019
  • Primary Citation of Related Structures:  
    1YQ5, 1YQ6, 1YQ8

  • PubMed Abstract: 

    Comparisons of bacteriophage PRD1 and adenovirus protein structures and virion architectures have been instrumental in unraveling an evolutionary relationship and have led to a proposal of a phylogeny-based virus classification. The structure of the PRD1 spike protein P5 provides further insight into the evolution of viral proteins. The crystallized P5 fragment comprises two structural domains: a globular knob and a fibrous shaft. The head folds into a ten-stranded jelly roll beta barrel, which is structurally related to the tumor necrosis factor (TNF) and the PRD1 coat protein domains. The shaft domain is a structural counterpart to the adenovirus spike shaft. The structural relationships between PRD1, TNF, and adenovirus proteins suggest that the vertex proteins may have originated from an ancestral TNF-like jelly roll coat protein via a combination of gene duplication and deletion.


  • Organizational Affiliation

    Programme on Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Viikinkaari 1 00014, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Minor capsid protein
A, B
144Enterobacteria phage PRD1Mutation(s): 2 
UniProt
Find proteins for P22536 (Enterobacteria phage PRD1)
Explore P22536 
Go to UniProtKB:  P22536
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22536
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.37α = 90
b = 114.37β = 90
c = 114.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary