4P1Y

Crystal structure of staphylococcal gamma-hemolysin prepore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

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:  
    4P1X, 4P1Y

  • 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 pores ...

    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

    1] Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan [2] Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-hemolysin component BA, C, E, G309Staphylococcus aureus subsp. aureus Mu50Mutation(s): 2 
Gene Names: hlgBSAV2421
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-hemolysin component AB, D, F, H290Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: hlgAhlg2SAV2419
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.056α = 90
b = 197.05β = 99.04
c = 192.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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