2G9H

Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human major histocompatibility complex class II molecule.

Fernandez, M.M.Guan, R.Swaminathan, C.P.Malchiodi, E.L.Mariuzza, R.A.

(2006) J.Biol.Chem. 281: 25356-25364

  • DOI: 10.1074/jbc.M603969200

  • PubMed Abstract: 
  • Superantigens are bacterial or viral proteins that elicit massive T cell activation through simultaneous binding to major histocompatibility complex (MHC) class II and T cell receptors. This activation results in uncontrolled release of inflammatory ...

    Superantigens are bacterial or viral proteins that elicit massive T cell activation through simultaneous binding to major histocompatibility complex (MHC) class II and T cell receptors. This activation results in uncontrolled release of inflammatory cytokines, causing toxic shock. A remarkable property of superantigens, which distinguishes them from T cell receptors, is their ability to interact with multiple MHC class II alleles independently of MHC-bound peptide. Previous crystallographic studies have shown that staphylococcal and streptococcal superantigens belonging to the zinc family bind to a high affinity site on the class II beta-chain. However, the basis for promiscuous MHC recognition by zinc-dependent superantigens is not obvious, because the beta-chain is polymorphic and the MHC-bound peptide forms part of the binding interface. To understand how zinc-dependent superantigens recognize MHC, we determined the crystal structure, at 2.0 A resolution, of staphylococcal enterotoxin I bound to the human class II molecule HLA-DR1 bearing a peptide from influenza hemagglutinin. Interactions between the superantigen and DR1 beta-chain are mediated by a zinc ion, and 22% of the buried surface of peptide.MHC is contributed by the peptide. Comparison of the staphylococcal enterotoxin I.peptide.DR1 structure with ones determined previously revealed that zinc-dependent superantigens achieve promiscuous binding to MHC by targeting conservatively substituted residues of the polymorphic beta-chain. Additionally, these superantigens circumvent peptide specificity by engaging MHC-bound peptides at their conformationally conserved N-terminal regions while minimizing sequence-specific interactions with peptide residues to enhance cross-reactivity.


    Organizational Affiliation

    Instituto de Estudios de la Inmunidad Humoral, Laboratorio de Inmunología Estructural, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
182Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-1 beta chain
B
190Homo sapiensGene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P04229
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
C
13Influenza A virus (strain A/England/878/1969 H3N2)Gene Names: HA
Find proteins for P04664 (Influenza A virus (strain A/England/878/1969 H3N2))
Go to UniProtKB:  P04664
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
extracellular enterotoxin type I
D
218Staphylococcus aureusN/A
Find proteins for Q52T95 (Staphylococcus aureus)
Go to UniProtKB:  Q52T95
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DIO
Query on DIO

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Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.395α = 90.00
b = 99.933β = 92.00
c = 72.917γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CrystalCleardata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description