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: 73362.36 
• Atom Count: 4795 
• Residue Count: 624 
• Unique protein chains: 4

2SEB

X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II

• DOI: 10.2210/pdb2SEB/pdb

• Classification: COMPLEX (MHC CLASS II/SUPERANTIGEN)
• Organism(s): Staphylococcus aureus, Homo sapiens
• Expression System: Drosophila


• Deposited: 1997-10-16 Released: 1998-01-28 
• Deposition Author(s): Dessen, A., Lawrence, C.M., Cupo, S., Zaller, D.M., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.229 

Literature

X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II.

Dessen, A., Lawrence, C.M., Cupo, S., Zaller, D.M., Wiley, D.C.

(1997) Immunity 7: 473-481

• PubMed: 9354468 


• PubMed Abstract: 
  

Genetic predisposition to rheumatoid arthritis (RA) is linked to the MHC class II allele HLA-DR4. The charge of the amino acid at DRbeta71 in the peptide-binding site appears to be critical in discriminating DR molecules linked to increased disease susceptibility. We have determined the 2.5 A x-ray structure of the DR4 molecule with the strongest linkage to RA (DRB1*0401) complexed with a human collagen II peptide. Details of a predicted salt bridge between lysine DRbeta71 and aspartic acid at the P4 peptide position suggest how it may participate in both antigen binding and TCR activation. A model is proposed for the DR4 recognition of collagen II (261-273), an antigen immunodominant in human-transgenic mouse models of RA.

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Organizational Affiliation: 

Laboratory of Molecular Medicine, The Children's Hospital, Boston, Massachusetts 02115, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN	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 CLASS II HISTOCOMPATIBILITY ANTIGEN	B	192	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens) Go to Gene View: HLA-DRB1 Go to UniProtKB:  P13760

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
ENTEROTOXIN TYPE B	D	239	Staphylococcus aureus	Mutation(s): 0  Gene Names: entB
Find proteins for P01552 (Staphylococcus aureus) Go to UniProtKB:  P01552

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PEPTIDE FROM COLLAGEN II	E	12	Homo sapiens	Mutation(s): 0  Gene Names: COL2A1
Find proteins for P02458 (Homo sapiens) Go to Gene View: COL2A1 Go to UniProtKB:  P02458

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 78.530	α = 90.00
b = 100.280	β = 90.00
c = 100.870	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-10-16 
• Released Date: 1998-01-28 
• Deposition Author(s): Dessen, A., Lawrence, C.M., Cupo, S., Zaller, D.M., Wiley, D.C.

Revision History 

• Version 1.0: 1998-01-28
  Type: Initial release
• Version 1.1: 2008-03-25
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance