3ANZ

Crystal Structure of alpha-hemolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.303 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal alpha-hemolysin into heptameric pore structure

Tanaka, Y.Hirano, N.Kaneko, J.Kamio, Y.Yao, M.Tanaka, I.

(2011) Protein Sci. 20: 448-456

  • DOI: 10.1002/pro.579

  • PubMed Abstract: 
  • Staphylococcal α-hemolysin is expressed as a water-soluble monomeric protein and assembles on membranes to form a heptameric pore structure. The heptameric pore structure of α-hemolysin can be prepared from monomer in vitro only in the presence of de ...

    Staphylococcal α-hemolysin is expressed as a water-soluble monomeric protein and assembles on membranes to form a heptameric pore structure. The heptameric pore structure of α-hemolysin can be prepared from monomer in vitro only in the presence of deoxycholate detergent micelles, artificially constructed phospholipid bilayers, or erythrocytes. Here, we succeeded in preparing crystals of the heptameric form of α-hemolysin without any detergent but with 2-methyl-2,4-pentanediol (MPD), and determined its structure. The structure of the heptameric pore was similar to that reported previously. In the structure, two molecules of MPD were bound around Trp179, around which phospholipid head groups were bound in the heptameric pore structure reported previously. Size exclusion chromatography showed that α-hemolysin did not assemble spontaneously even when stored for 1 year. SDS-PAGE analysis revealed that, among the compounds in the crystallizing buffer, MPD could induce heptamer formation. The concentration of MPD that most efficiently induced oligomerization was between 10 and 30%. Based on these observations, we propose MPD as a reagent that can facilitate heptameric pore formation of α-hemolysin without membrane binding.


    Organizational Affiliation

    Creative Research Institution Sousei, Hokkaido University, Sapporo 001-0021, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-hemolysin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b
302Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
α-hemolysin
Find proteins for A0A0H3JRX7 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  A0A0H3JRX7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, a, b, C, D, E, F, H, J, K, L, M, O, P, Q, S, T, V, W, X, Y, Z
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, a, b, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.303 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.821α = 90.00
b = 293.877β = 92.42
c = 170.545γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Other
  • Version 1.3: 2017-10-11
    Type: Refinement description