3QR8

Crystal structure of the bacteriophage P2 membrane-piercing protein gpV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.260 

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
Baseplate assembly protein V
A
211Escherichia phage P2Mutation(s): 0 
Gene Names: V
Find proteins for P31340 (Escherichia phage P2)
Go to UniProtKB:  P31340
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
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
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.260 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.539α = 90.00
b = 68.539β = 90.00
c = 132.180γ = 120.00
Software Package:
Software NamePurpose
RemDAqdata collection
PHENIXrefinement
SHELXmodel building
SHELXphasing
SCALAdata scaling
MOSFLMdata reduction

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: Advisory, Refinement description