4P1X

Crystal structure of staphylococcal LUK prepore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.

Yamashita, D.Sugawara, T.Takeshita, M.Kaneko, J.Kamio, Y.Tanaka, I.Tanaka, Y.Yao, M.

(2014) Nat Commun 5: 4897-4897

  • DOI: 10.1038/ncomms5897
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pathogenic bacteria secrete pore-forming toxins (PFTs) to attack target cells. PFTs are expressed as water-soluble monomeric proteins, which oligomerize into nonlytic prepore intermediates on the target cell membrane before forming membrane-spanning ...

    Pathogenic bacteria secrete pore-forming toxins (PFTs) to attack target cells. PFTs are expressed as water-soluble monomeric proteins, which oligomerize into nonlytic prepore intermediates on the target cell membrane before forming membrane-spanning pores. Despite a wealth of biochemical data, the lack of high-resolution prepore structural information has hampered understanding of the β-barrel formation process. Here, we report crystal structures of staphylococcal γ-haemolysin and leucocidin prepores. The structures reveal a disordered bottom half of the β-barrel corresponding to the transmembrane region, and a rigid upper extramembrane half. Spectroscopic analysis of fluorescently labelled mutants confirmed that the prepore is distinct from the pore within the transmembrane region. Mutational analysis also indicates a pivotal role for the glycine residue located at the lipid-solvent interface as a 'joint' between the two halves of the β-barrel. These observations suggest a two-step transmembrane β-barrel pore formation mechanism in which the upper extramembrane and bottom transmembrane regions are formed independently.


    Organizational Affiliation

    Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.,Department of Human Health and Nutrition, Graduate School of Comprehensive Human Sciences, Shokei Gakuin University, Yurigaoka 4-10-1, Natori 981-1295, Japan.,1] Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan [2] Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-hemolysin component C
B, D, F, H
296Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: hlgC
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 Q99RL1 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  Q99RL1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-hemolysin component B
A, C, E, G
309Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 1 
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
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: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 193.310α = 90.00
b = 193.160β = 118.94
c = 116.380γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references