4IDJ

S.Aureus a-hemolysin monomer in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of Action and In Vivo Efficacy of a Human-Derived Antibody against Staphylococcus aureus alpha-Hemolysin.

Foletti, D.Strop, P.Shaughnessy, L.Hasa-Moreno, A.Casas, M.G.Russell, M.Bee, C.Wu, S.Pham, A.Zeng, Z.Pons, J.Rajpal, A.Shelton, D.

(2013) J Mol Biol 425: 1641-1654

  • DOI: https://doi.org/10.1016/j.jmb.2013.02.008
  • Primary Citation of Related Structures:  
    4IDJ

  • PubMed Abstract: 

    The emergence and spread of multi-drug-resistant strains of Staphylococcus aureus in hospitals and in the community emphasize the urgency for the development of novel therapeutic interventions. Our approach was to evaluate the potential of harnessing the human immune system to guide the development of novel therapeutics. We explored the role of preexisting antibodies against S. aureus α-hemolysin in the serum of human individuals by isolating and characterizing one antibody with a remarkably high affinity to α-hemolysin. The antibody provided protection in S. aureus pneumonia, skin, and bacteremia mouse models of infection and also showed therapeutic efficacy when dosed up to 18 h post-infection in the pneumonia model. Additionally, in pneumonia and bacteremia animal models, the therapeutic efficacy of the α-hemolysin antibody appeared additive to the antibiotic linezolid. To better understand the mechanism of action of this isolated antibody, we solved the crystal structure of the α-hemolysin:antibody complex. To our knowledge, this is the first report of the crystal structure of the α-hemolysin monomer. The structure of the complex shows that the antibody binds α-hemolysin between the cap and the rim domains. In combination with biochemical data, the structure suggests that the antibody neutralizes the activity of the toxin by preventing binding to the plasma membrane of susceptible host cells. The data presented here suggest that protective antibodies directed against S. aureus molecules exist in some individuals and that such antibodies have a therapeutic potential either alone or in combination with antibiotics.


  • Organizational Affiliation

    Rinat Laboratories, Pfizer Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA. davide.foletti@pfizer.com


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-hemolysin295Staphylococcus aureusMutation(s): 0 
Gene Names: hlahly
UniProt
Find proteins for P09616 (Staphylococcus aureus)
Explore P09616 
Go to UniProtKB:  P09616
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09616
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy chainB [auth H]239Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light chainC [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.188α = 90
b = 130.188β = 90
c = 308.336γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2013-06-26 
  • Deposition Author(s): Strop, P.

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Source and taxonomy
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2021-05-26
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary