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: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.224 
  • R-Value Observed: 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

  • DOI: 10.1016/s1074-7613(01)00092-9
  • Primary Citation of Related Structures:  
    1HQR

  • 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 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) ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-DR ALPHA CHAINA181Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
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Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
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UniProt GroupP01903
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-DR BETA CHAINB190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB5
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Find proteins for Q30154 (Homo sapiens)
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PHAROS:  Q30154
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UniProt GroupQ30154
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MYELIN BASIC PROTEINC13Homo sapiensMutation(s): 0 
Gene Names: MBP
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Find proteins for P02686 (Homo sapiens)
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Go to UniProtKB:  P02686
PHAROS:  P02686
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UniProt GroupP02686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
STREPTOCOCCAL PYROGENIC EXOTOXIN CD208Streptococcus pyogenesMutation(s): 0 
UniProt
Find proteins for Q8NKX2 (Streptococcus pyogenes serotype M18 (strain MGAS8232))
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Go to UniProtKB:  Q8NKX2
Entity Groups  
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UniProt GroupQ8NKX2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.827α = 90
b = 111.95β = 90
c = 216.617γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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