3ANZ

Crystal Structure of alpha-hemolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1002/pro.579
  • Primary Citation of Related Structures:  
    3ANZ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-hemolysin
A,
AA [auth a],
B,
BA [auth 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
302Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: hlahlySAV1163
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3JRX7 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JRX7 
Go to UniProtKB:  A0A0H3JRX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JRX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AC [auth Q]
AD [auth Z]
BB [auth I]
CA [auth A]
CB [auth I]
AC [auth Q],
AD [auth Z],
BB [auth I],
CA [auth A],
CB [auth I],
CC [auth R],
CD [auth a],
DA [auth A],
DB [auth J],
DC [auth R],
DD [auth a],
EB [auth J],
EC [auth S],
FC [auth S],
FD [auth b],
GA [auth B],
GB [auth K],
GD [auth b],
HA [auth B],
HB [auth K],
IA [auth C],
IC [auth T],
JA [auth C],
JC [auth T],
KB [auth L],
LA [auth D],
LB [auth L],
LC [auth U],
MA [auth D],
MC [auth U],
NB [auth M],
NC [auth V],
OB [auth M],
OC [auth V],
PA [auth E],
QA [auth E],
QB [auth N],
QC [auth W],
RB [auth N],
RC [auth W],
SA [auth F],
SB [auth O],
TA [auth F],
TB [auth O],
TC [auth X],
UC [auth X],
VA [auth G],
VC [auth X],
WA [auth G],
WB [auth P],
XA [auth H],
XB [auth P],
XC [auth Y],
YA [auth H],
YC [auth Y],
ZB [auth Q]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
AB [auth H]
BC [auth Q]
BD [auth Z]
EA [auth A]
ED [auth a]
AB [auth H],
BC [auth Q],
BD [auth Z],
EA [auth A],
ED [auth a],
FA [auth A],
FB [auth J],
GC [auth S],
HC [auth S],
HD [auth b],
IB [auth K],
JB [auth K],
KA [auth C],
KC [auth T],
MB [auth L],
NA [auth D],
OA [auth D],
PB [auth M],
PC [auth V],
RA [auth E],
SC [auth W],
UA [auth F],
UB [auth O],
VB [auth O],
WC [auth X],
YB [auth P],
ZA [auth H],
ZC [auth Y]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.821α = 90
b = 293.877β = 92.42
c = 170.545γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Other
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description