1DEE

Structure of S. aureus protein A bound to a human IgM Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.

Graille, M., Stura, E.A., Corper, A.L., Sutton, B.J., Taussig, M.J., Charbonnier, J.B., Silverman, G.J.

(2000) Proc Natl Acad Sci U S A 97: 5399-5404

  • DOI: 10.1073/pnas.97.10.5399
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Staphylococcus aureus produces a virulence factor, protein A (SpA), that contains five homologous Ig-binding domains. The interactions of SpA with the Fab region of membrane-anchored Igs can stimulate a large fraction of B cells, contributing to lymp ...

    Staphylococcus aureus produces a virulence factor, protein A (SpA), that contains five homologous Ig-binding domains. The interactions of SpA with the Fab region of membrane-anchored Igs can stimulate a large fraction of B cells, contributing to lymphocyte clonal selection. To understand the molecular basis for this activity, we have solved the crystal structure of the complex between domain D of SpA and the Fab fragment of a human IgM antibody to 2.7-A resolution. In the complex, helices II and III of domain D interact with the variable region of the Fab heavy chain (V(H)) through framework residues, without the involvement of the hypervariable regions implicated in antigen recognition. The contact residues are highly conserved in human V(H)3 antibodies but not in other families. The contact residues from domain D also are conserved among all SpA Ig-binding domains, suggesting that each could bind in a similar manner. Features of this interaction parallel those reported for staphylococcal enterotoxins that are superantigens for many T cells. The structural homology between Ig V(H) regions and the T-cell receptor V(beta) regions facilitates their comparison, and both types of interactions involve lymphocyte receptor surface remote from the antigen binding site. However, T-cell superantigens reportedly interact through hydrogen bonds with T-cell receptor V(beta) backbone atoms in a primary sequence-independent manner, whereas SpA relies on a sequence-restricted conformational binding with residue side chains, suggesting that this common bacterial pathogen has adopted distinct molecular recognition strategies for affecting large sets of B and T lymphocytes.

    Organizational Affiliation: 

    Département d'Ingénierie et d'Etudes des Protéines (DIEP), Commissariat à l'Energie Atomique (CEA), C.E. Saclay, 91191 Gif-sur-Yvette Cedex, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGM RF 2A2
A, C, E
214Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGM RF 2A2
B, D, F
223Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN G BINDING PROTEIN A
G, H
54Staphylococcus aureusMutation(s): 0 
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P02976
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.52α = 90
b = 78.91β = 100.71
c = 163.24γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-14
    Changes: Structure summary