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 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-DR BETA CHAIN
B
190Homo sapiensGene 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 sapiensGene 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)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



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