1HQR

CRYSTAL STRUCTURE OF A SUPERANTIGEN BOUND TO THE HIGH-AFFINITY, ZINC-DEPENDENT SITE ON MHC CLASS II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II.

Li, Y., Li, H., Dimasi, N., McCormick, J.K., Martin, R., Schuck, P., Schlievert, P.M., Mariuzza, R.A.

(2001) Immunity 14: 93-104


  • PubMed Abstract: 

    • MHC class II molecules possess two binding sites for bacterial superantigens (SAGs): a low-affinity site on the alpha chain and a high-affinity, zinc-dependent site on the beta chain. Only the former has been defined crystallographically. We report t ...

    MHC class II molecules possess two binding sites for bacterial superantigens (SAGs): a low-affinity site on the alpha chain and a high-affinity, zinc-dependent site on the beta chain. Only the former has been defined crystallographically. We report the structure of streptococcal pyrogenic exotoxin C (SPE-C) complexed with HLA-DR2a (DRA*0101, DRB5*0101) bearing a self-peptide from myelin basic protein (MBP). SPE-C binds the beta chain through a zinc bridge that links the SAG and class II molecules. Surprisingly, SPE-C also makes extensive contacts with the MBP peptide, such that peptide accounts for one third of the surface area of the MHC molecule buried in the complex, similar to TCR-peptide/MHC complexes. Thus, SPE-C may optimize T cell responses by mimicking the peptide dependence of conventional antigen presentation and recognition.

    Organizational Affiliation: 

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA-DR ALPHA CHAIN
A
181Homo sapiensMutation(s): 0 
Gene 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-DR BETA CHAIN
B
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB5
Find proteins for Q30154 (Homo sapiens)
Go to Gene View: HLA-DRB5
Go to UniProtKB:  Q30154
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MYELIN BASIC PROTEIN
C
13Homo sapiensMutation(s): 0 
Gene Names: MBP
Find proteins for P02686 (Homo sapiens)
Go to Gene View: MBP
Go to UniProtKB:  P02686
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
STREPTOCOCCAL PYROGENIC EXOTOXIN C
D
208Streptococcus pyogenes serotype M18 (strain MGAS8232)Mutation(s): 0 
Gene Names: speC
Find proteins for Q8NKX2 (Streptococcus pyogenes serotype M18 (strain MGAS8232))
Go to UniProtKB:  Q8NKX2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.224 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.827α = 90.00
b = 111.950β = 90.00
c = 216.617γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance