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 7F5K | pdb_00007f5k

Crystal structure of TCR4-1 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.311 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7F5K

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 96.97 kDa 
  • Atom Count: 6,678 
  • Modeled Residue Count: 856 
  • Deposited Residue Count: 876 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
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
Find similar proteins by:|  3D Structure
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 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
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

View Full Validation Report



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
  • Version 1.3: 2024-11-13
    Changes: Structure summary