Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69324.94 
• Atom Count: 4539 
• Residue Count: 592 
• Unique protein chains: 4

1HQR

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

• DOI: 10.2210/pdb1HQR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Streptococcus pyogenes serotype M18 (strain MGAS8232)
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)


• Deposited: 2000-12-19 Released: 2001-01-03 
• Deposition Author(s): Li, Y., Li, H., Dimasi, N., Schlievert, P., Mariuzza, R.

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Experimental Data Snapshot

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

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: 11163233 


• 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). 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
HLA-DR ALPHA CHAIN	A	181	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
HLA-DR BETA CHAIN	B	190	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
MYELIN BASIC PROTEIN	C	13	Homo sapiens	Mutation(s): 0  Gene Names: MBP
Find proteins for P02686 (Homo sapiens) Go to Gene View: MBP Go to UniProtKB:  P02686

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
STREPTOCOCCAL PYROGENIC EXOTOXIN C	D	208	Streptococcus 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 61.827	α = 90.00
b = 111.950	β = 90.00
c = 216.617	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-12-19 
• Released Date: 2001-01-03 
• Deposition Author(s): Li, Y., Li, H., Dimasi, N., Schlievert, P., Mariuzza, R.

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