7F5K

Crystal structure of TCR4-1 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b.

Shibata, K.Motozono, C.Nagae, M.Shimizu, T.Ishikawa, E.Motooka, D.Okuzaki, D.Izumi, Y.Takahashi, M.Fujimori, N.Wing, J.B.Hayano, T.Asai, Y.Bamba, T.Ogawa, Y.Furutani-Seiki, M.Shirai, M.Yamasaki, S.

(2022) Nat Commun 13: 6948-6948

  • DOI: https://doi.org/10.1038/s41467-022-34802-8
  • Primary Citation of Related Structures:  
    7F5K

  • PubMed Abstract: 

    MHC class I-related protein 1 (MR1) is a metabolite-presenting molecule that restricts MR1-reactive T cells including mucosal-associated invariant T (MAIT) cells. In contrast to MAIT cells, the function of other MR1-restricted T cell subsets is largely unknown. Here, we report that mice in which a T cell-specific transcription factor, B-cell lymphoma/leukemia 11B (Bcl11b), was ablated in immature thymocytes (Bcl11b ∆iThy mice) develop chronic inflammation. Bcl11b ∆iThy mice lack conventional T cells and MAIT cells, whereas CD4 + IL-18R + αβ T cells expressing skewed Traj33 (Jα33) + T cell receptors (TCR) accumulate in the periphery, which are necessary and sufficient for the pathogenesis. The disorders observed in Bcl11b ∆iThy mice are ameliorated by MR1-deficiency, transfer of conventional T cells, or germ-free conditions. We further show the crystal structure of the TCR expressed by Traj33 + T cells expanded in Bcl11b ∆iThy mice. Overall, we establish that MR1-reactive T cells have pathogenic potential.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha chain
A, C
200Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta chain
B, D
238Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.874α = 90
b = 73.79β = 90
c = 170.337γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description