3B07

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 

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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 U S A 108: 17314-17319

  • DOI: 10.1073/pnas.1110402108
  • Primary Citation of Related Structures:  
    3B07

  • 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 of the octameric pore form of γ-hemolysin at 2 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-hemolysin component BA,
B [auth C],
C [auth E],
D [auth G]
309Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SAV2421hlgB
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H3JX61 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JX61 
Go to UniProtKB:  A0A0H3JX61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JX61
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-hemolysin component AE [auth B],
F [auth D],
G [auth F],
H
290Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SAV2419hlgAhlg2
Membrane Entity: Yes 
UniProt
Find proteins for P0A071 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A071 
Go to UniProtKB:  P0A071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A071
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A],
J [auth C],
K [auth E],
L [auth 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: 2.50 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
b = 206.141β = 90
c = 190.299γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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