3PQI

Crystal structure of the bacteriophage phi92 membrane-piercing protein gp138


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.642 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Phage pierces the host cell membrane with the iron-loaded spike.

Browning, C.Shneider, M.M.Bowman, V.D.Schwarzer, D.Leiman, P.G.

(2012) Structure 20: 326-339

  • DOI: 10.1016/j.str.2011.12.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteriophages with contractile tails and the bacterial type VI secretion system have been proposed to use a special protein to create an opening in the host cell membrane during infection. These proteins have a modular architecture but invariably co ...

    Bacteriophages with contractile tails and the bacterial type VI secretion system have been proposed to use a special protein to create an opening in the host cell membrane during infection. These proteins have a modular architecture but invariably contain an oligonucleotide/oligosaccharide-binding (OB-fold) domain and a long β-helical C-terminal domain, which initiates the contact with the host cell membrane. Using X-ray crystallography and electron microscopy, we report the atomic structure of the membrane-piercing proteins from bacteriophages P2 and ϕ92 and identify the residues that constitute the membrane-attacking apex. Both proteins form compact spikes with a ∼10Å diameter tip that is stabilized by a centrally positioned iron ion bound by six histidine residues. The accumulated data strongly suggest that, in the process of membrane penetration, the spikes are translocated through the lipid bilayer without undergoing major unfolding.


    Organizational Affiliation

    Institut de Physique des Systèmes Biologiques, Laboratory of Structural Biology and Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), BSP-415, CH-1015, Lausanne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
gene product 138
A
247Enterobacteria phage phi92Mutation(s): 0 
Gene Names: PHI92_gene_138
Find proteins for I7HXF9 (Enterobacteria phage phi92)
Go to UniProtKB:  I7HXF9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.642 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 65.144α = 90.00
b = 65.144β = 90.00
c = 329.375γ = 120.00
Software Package:
Software NamePurpose
RemDAqdata collection
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description