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 

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This is version 1.4 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
  • Primary Citation of Related Structures:  
    3PL6

  • 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) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chainA194Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt
Find proteins for A0A173ADG5 (Homo sapiens)
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Go to UniProtKB:  A0A173ADG5
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UniProt GroupA0A173ADG5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II HLA-DQ-beta chainB202Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for A0A0A8WFP6 (Homo sapiens)
Explore A0A0A8WFP6 
Go to UniProtKB:  A0A0A8WFP6
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UniProt GroupA0A0A8WFP6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha chainC206Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MBP peptide / T-cell receptor beta chain chimeraD268Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
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
b = 124.815β = 90
c = 134.921γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary