3PL6

Structure of Autoimmune TCR Hy.1B11 in complex with HLA-DQ1 and MBP 85-99


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC.

Sethi, D.K.Schubert, D.A.Anders, A.K.Heroux, A.Bonsor, D.A.Thomas, C.P.Sundberg, E.J.Pyrdol, J.Wucherpfennig, K.W.

(2011) J.Exp.Med. 208: 91-102

  • DOI: 10.1084/jem.20100725

  • PubMed Abstract: 
  • Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) ...

    Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-α chain with the MHC class II β chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3β loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3α loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-alpha chain
A
194Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for A0A173ADG5 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  A0A173ADG5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-beta chain
B
202Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for A0A0A8WFP6 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  A0A0A8WFP6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha chain
C
206N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MBP peptide / T-cell receptor beta chain chimera
D
268N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.123α = 90.00
b = 124.815β = 90.00
c = 134.921γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Source and taxonomy
  • Version 1.3: 2017-11-08
    Type: Refinement description