3ANZ | pdb_00003anz

Crystal Structure of alpha-hemolysin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.226 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 974.48 kDa 
  • Atom Count: 68,607 
  • Modeled Residue Count: 8,243 
  • Deposited Residue Count: 8,456 
  • Unique protein chains: 1

Macromolecules

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|  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: hla, hly, SAV1163
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
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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 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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

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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