Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.52 kDa 
• Atom Count: 5789 
• Modelled Residue Count: 716 
• Deposited Residue Count: 868 
• Unique protein chains: 5

1YMM

TCR/HLA-DR2b/MBP-peptide complex

• PDB DOI: 10.2210/pdb1YMM/pdb

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


• 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: 3.50 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 

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
• Primary Citation of Related Structures:  
  1YMM


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	191	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR beta chain	B	198	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MBP peptide	C	23	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02686 (Homo sapiens) Explore P02686  Go to UniProtKB:  P02686
PHAROS:  P02686 GTEx:  ENSG00000197971

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	D	207	Homo sapiens	Mutation(s): 0  Gene Names: TRAC, TCRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.34	α = 90
b = 212.62	β = 90
c = 278.22	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Structure summary