3B07

Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.495 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the octameric pore of staphylococcal gamma-hemolysin reveals the beta-barrel pore formation mechanism by two components

Yamashita, K.Kawai, Y.Tanaka, Y.Hirano, N.Kaneko, J.Tomita, N.Ohta, M.Kamio, Y.Yao, M.Tanaka, I.

(2011) Proc.Natl.Acad.Sci.USA 108: 17314-17319

  • DOI: 10.1073/pnas.1110402108

  • PubMed Abstract: 
  • Staphylococcal γ-hemolysin is a bicomponent pore-forming toxin composed of LukF and Hlg2. These proteins are expressed as water-soluble monomers and then assemble into the oligomeric pore form on the target cell. Here, we report the crystal structure ...

    Staphylococcal γ-hemolysin is a bicomponent pore-forming toxin composed of LukF and Hlg2. These proteins are expressed as water-soluble monomers and then assemble into the oligomeric pore form on the target cell. Here, we report the crystal structure of the octameric pore form of γ-hemolysin at 2.5 Å resolution, which is the first high-resolution structure of a β-barrel transmembrane protein composed of two proteins reported to date. The octameric assembly consists of four molecules of LukF and Hlg2 located alternately in a circular pattern, which explains the biochemical data accumulated over the past two decades. The structure, in combination with the monomeric forms, demonstrates the elaborate molecular machinery involved in pore formation by two different molecules, in which interprotomer electrostatic interactions using loops connecting β2 and β3 (loop A: Asp43-Lys48 of LukF and Lys37-Lys43 of Hlg2) play pivotal roles as the structural determinants for assembly through unwinding of the N-terminal β-strands (amino-latch) of the adjacent protomer, releasing the transmembrane stem domain folded into a β-sheet in the monomer (prestem), and interaction with the adjacent protomer.


    Organizational Affiliation

    Graduate School of Life Science , Hokkaido University, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-hemolysin component B
A, C, E, G
309Staphylococcus aureus (strain Mu50 / ATCC 700699)Gene Names: hlgB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
γ-hemolysin composed of LukF and Hlg2
Find proteins for A0A0H3JX61 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  A0A0H3JX61
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-hemolysin component A
B, D, F, H
290Staphylococcus aureus (strain Mu50 / ATCC 700699)Gene Names: hlgA (hlg2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
γ-hemolysin composed of LukF and Hlg2
Find proteins for P0A071 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P0A071
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C, E, G
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.495 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 206.454α = 90.00
b = 206.141β = 90.00
c = 190.299γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BSSdata collection
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-12-21
    Type: Database references