Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN S component from STAPHYLOCOCCUS AUREUS

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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This is version 1.3 of the entry. See complete history


Residues essential for panton-valentine leukocidin s component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface

Laventie, B.J.Guerin, F.Mourey, L.Tawk, M.Y.Jover, E.Maveyraud, L.Prevost, G.

(2014) PLoS One 9: e92094-e92094

  • DOI: https://doi.org/10.1371/journal.pone.0092094
  • Primary Citation of Related Structures:  
    4IYA, 4IYC, 4IYT, 4IZL, 4J0O

  • PubMed Abstract: 

    Panton-Valentine leukocidin (PVL), a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The class S component of PVL, LukS-PV, is known to ensure cell targeting and exhibits the highest affinity for the neutrophil membrane (Kd∼10(-10) M) compared to the class F component of PVL, LukF-PV (Kd∼10(-9) M). Alanine scanning mutagenesis was used to identify the residues involved in LukS-PV binding to the neutrophil surface. Nineteen single alanine mutations were performed in the rim domain previously described as implicated in cell membrane interactions. Positions were chosen in order to replace polar or exposed charged residues and according to conservation between leukotoxin class S components. Characterization studies enabled to identify a cluster of residues essential for LukS-PV binding, localized on two loops of the rim domain. The mutations R73A, Y184A, T244A, H245A and Y250A led to dramatically reduced binding affinities for both human leukocytes and undifferentiated U937 cells expressing the C5a receptor. The three-dimensional structure of five of the mutants was determined using X-ray crystallography. Structure analysis identified residues Y184 and Y250 as crucial in providing structural flexibility in the receptor-binding domain of LukS-PV.

  • Organizational Affiliation

    Université de Strasbourg-CHRU, Fédération de Médecine Translationnelle de Strasbourg, EA 7290 Virulence bactérienne précoce, Institut de Bactériologie, Strasbourg, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LukS-PV292Staphylococcus phage PVLMutation(s): 1 
Find proteins for O80066 (Staphylococcus phage PVL)
Explore O80066 
Go to UniProtKB:  O80066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO80066
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.34α = 90
b = 89.32β = 90
c = 38.1γ = 90
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2014-04-23
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description