1YMM

TCR/HLA-DR2b/MBP-peptide complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 t ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
191Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR beta chain
B
198Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
MBP peptide
C
23Homo sapiensMutation(s): 0 
Gene Names: MBP
Find proteins for P02686 (Homo sapiens)
Go to Gene View: MBP
Go to UniProtKB:  P02686
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T cell receptor alpha chain
D
207Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor beta chain
E
249Homo sapiensMutation(s): 2 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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 = 137.340α = 90.00
b = 212.620β = 90.00
c = 278.220γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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