Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98519.68 
• Atom Count: 5789 
• Residue Count: 868 
• Unique protein chains: 5

1YMM

TCR/HLA-DR2b/MBP-peptide complex

• DOI: 10.2210/pdb1YMM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): 2 


• Deposited: 2005-01-21 Released: 2005-05-03 
• Deposition Author(s): Hahn, M., Nicholson, M.J., Pyrdol, J., Wucherpfennig, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 

Literature

Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor.

Hahn, M., Nicholson, M.J., Pyrdol, J., Wucherpfennig, K.W.

(2005) NAT.IMMUNOL. 6: 490-496

• PubMed: 15821740 
• DOI: 10.1038/ni1187


• PubMed Abstract: 
  

Autoimmune diseases are caused by self-reactive lymphocytes that have escaped deletion. Here we have determined the structure of the trimolecular complex for a T cell receptor (TCR) from a patient with multiple sclerosis that causes autoimmunity in transgenic mice. The structure showed a TCR topology notably different from that of antimicrobial TCRs. Rather than being centered on the peptide-major histocompatibility complex, this TCR contacted only the N-terminal peptide segment and made asymmetrical interactions with the major histocompatibility complex helices. The interaction was dominated by the hypervariable complementarity-determining region 3 loops, indicating that unconventional topologies are possible because of the unique complementarity-determining region 3 sequences created during rearrangement. This topology reduces the interaction surface with peptide and alters the geometry for CD4 association. We propose that unusual TCR-binding properties can permit autoreactive T cells to escape deletion.

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Organizational Affiliation: 

Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A	191	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, DR beta chain	B	198	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1 (HLA-DRB2)
Find proteins for P01911 (Homo sapiens) Go to Gene View: HLA-DRB1 Go to UniProtKB:  P01911

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MBP peptide	C	23	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
T cell receptor alpha chain	D	207	Homo sapiens	Mutation(s): 0  Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens) Go to UniProtKB:  P01848

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
T-cell receptor beta chain	E	249	Homo sapiens	Mutation(s): 2  Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens) Go to UniProtKB:  P01850

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: 3.5 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 
• Space Group: F 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 137.340	α = 90.00
b = 212.620	β = 90.00
c = 278.220	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
PHASER	phasing
SCALEPACK	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-21 
• Released Date: 2005-05-03 
• Deposition Author(s): Hahn, M., Nicholson, M.J., Pyrdol, J., Wucherpfennig, K.W.

Revision History 

• Version 1.0: 2005-05-03
  Type: Initial release
• Version 1.1: 2007-10-16
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance