4UW7

Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber without its intra-molecular chaperone domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.

Garcia-Doval, C.Caston, J.R.Luque, D.Granell, M.Otero, J.M.Llamas-Saiz, A.L.Renouard, M.Boulanger, P.van Raaij, M.J.

(2015) Viruses 7: 6424-6440

  • DOI: 10.3390/v7122946
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection an ...

    Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970-1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263-1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition.


    Related Citations: 
    • Crystallization of the C-Terminal Domain of the Bacteriophage T5 L-Shaped Fibre.
      Garcia-Doval, C.,Luque, D.,Caston, J.R.,Boulanger, P.,van Raaij, M.J.
      (2013) Acta Crystallogr.,Sect.F 69: 1363


    Organizational Affiliation

    Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain. c.garcia@bioc.uzh.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-SHAPED TAIL FIBER PROTEIN
A, B, C
294Escherichia phage T5Mutation(s): 0 
Gene Names: ltf
EC: 3.4.21.-
Find proteins for P13390 (Escherichia phage T5)
Go to UniProtKB:  P13390
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 227.430α = 90.00
b = 58.180β = 98.81
c = 69.910γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
autoSHARPphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references, Structure summary
  • Version 1.2: 2015-12-30
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Database references