4JMQ

Crystal structure of pb9: The Dit of bacteriophage T5.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of pb9, the Distal Tail Protein of Bacteriophage T5: a Conserved Structural Motif among All Siphophages.

Flayhan, A.Vellieux, F.M.Lurz, R.Maury, O.Contreras-Martel, C.Girard, E.Boulanger, P.Breyton, C.

(2014) J.Virol. 88: 820-828

  • DOI: 10.1128/JVI.02135-13
  • Also Cited By: 5MF2

  • PubMed Abstract: 
  • The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process tha ...

    The tail of Caudovirales bacteriophages serves as an adsorption device, a host cell wall-perforating machine, and a genome delivery pathway. In Siphoviridae, the assembly of the long and flexible tail is a highly cooperative and regulated process that is initiated from the proteins forming the distal tail tip complex. In Gram-positive-bacterium-infecting siphophages, the distal tail (Dit) protein has been structurally characterized and is proposed to represent a baseplate hub docking structure. It is organized as a hexameric ring that connects the tail tube and the adsorption device. In this study, we report the characterization of pb9, a tail tip protein of Escherichia coli bacteriophage T5. By immunolocalization, we show that pb9 is located in the upper part of the cone of the T5 tail tip, at the end of the tail tube. The crystal structure of pb9 reveals a two-domain protein. Domain A exhibits remarkable structural similarity with the N-terminal domain of known Dit proteins, while domain B adopts an oligosaccharide/oligonucleotide-binding fold (OB-fold) that is not shared by these proteins. We thus propose that pb9 is the Dit protein of T5, making it the first Dit protein described for a Gram-negative-bacterium-infecting siphophage. Multiple sequence alignments suggest that pb9 is a paradigm for a large family of Dit proteins of siphophages infecting mostly Gram-negative hosts. The modular structure of the Dit protein maintains the basic building block that would be conserved among all siphophages, combining it with a more divergent domain that might serve specific host adhesion properties.


    Organizational Affiliation

    Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriophage T5 distal tail protein
A, B, C, D
217Escherichia phage T5Gene Names: D16
Find proteins for Q6QGE8 (Escherichia phage T5)
Go to UniProtKB:  Q6QGE8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.657α = 91.05
b = 70.027β = 107.66
c = 71.014γ = 112.03
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Database references