Biological Assembly 1  

 3D View: Structure

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 144.65 kDa 
• Atom Count: 9396 
• Modelled Residue Count: 1184 
• Deposited Residue Count: 1240 
• Unique protein chains: 4

1SEB

COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BACTERIAL SUPERANTIGEN SEB

• DOI: 10.2210/pdb1SEB/pdb

• Classification: COMPLEX (MHC II/PEPTIDE/TOXIN)
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 1995-11-26 Released: 1996-06-20 
• Deposition Author(s): Jardetzky, T.S., Brown, J.H., Gorga, J.C., Stern, L.J., Urban, R.G., Chi, Y.I., Stauffacher, C., Strominger, J.L., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.327 
• R-Value Work: 0.257 
• R-Value Observed: 0.257 

Literature

Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen.

Jardetzky, T.S., Brown, J.H., Gorga, J.C., Stern, L.J., Urban, R.G., Chi, Y.I., Stauffacher, C., Strominger, J.L., Wiley, D.C.

(1994) Nature 368: 711-718

• PubMed: 8152483 
• DOI: 10.1038/368711a0
• Primary Citation of Related Structures:  
  1SEB


• PubMed Abstract: 
  

The structure of a bacterial superantigen, Staphylococcus aureus enterotoxin B, bound to a human class II histocompatibility complex molecule (HLA-DR1) has been determined by X-ray crystallography. The superantigen binds as an intact protein outside the conventional peptide antigen-binding site of the class II major histocompatibility complex (MHC) molecule. No large conformational changes occur upon complex formation in either the DR1 or the enterotoxin B molecules. The structure of the complex helps explain how different class II molecules and superantigens associate and suggests a model for ternary complex formation with the T-cell antigen receptor (TCR), in which unconventional TCR-MHC contacts are possible.

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Related Citations: 

• Crystallographic Analysis of Endogenous Peptides Associated with Hla-Dr1 Suggests a Common, Polyproline II-Like Conformation for Bound Peptides
  Jardetzky, T.S., Brown, J.H., Gorga, J.C., Stern, L.J., Urban, R.G., Strominger, J.L., Wiley, D.C.
  (1996) Proc Natl Acad Sci U S A 93: 734

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN	A, E	181	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN	B, F	192	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGENOUS PEPTIDE MODEL, POLY-ALA	C, G	13	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ENTEROTOXIN TYPE B	D, H	234	Staphylococcus aureus	Mutation(s): 0  Gene Names: entB
Find proteins for P01552 (Staphylococcus aureus) Explore P01552  Go to UniProtKB:  P01552

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.327 
• R-Value Work: 0.257 
• R-Value Observed: 0.257 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95	α = 90
b = 114.7	β = 90
c = 149.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-11-26 
• Released Date: 1996-06-20 
Deposition Author(s): Jardetzky, T.S., Brown, J.H., Gorga, J.C., Stern, L.J., Urban, R.G., Chi, Y.I., Stauffacher, C., Strominger, J.L., Wiley, D.C.

Revision History  

• Version 1.0: 1996-06-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance