4JJ2

High resolution structure of a C-terminal fragment of the T4 phage gp5 beta-helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4.

Buth, S.A.Menin, L.Shneider, M.M.Engel, J.Boudko, S.P.Leiman, P.G.

(2015) Viruses 7: 4676-4706

  • DOI: https://doi.org/10.3390/v7082839
  • Primary Citation of Related Structures:  
    4JJ2, 4OSD

  • PubMed Abstract: 

    Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.


  • Organizational Affiliation

    Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland. sergii.buth@epfl.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tail-associated lysozyme
A, B, C
95Tequatrovirus T4Mutation(s): 0 
Gene Names: 5
EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4)
Explore P16009 
Go to UniProtKB:  P16009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16009
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.609α = 90
b = 72.764β = 90
c = 130.49γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-02-08
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection