8XUB | pdb_00008xub

Crystal structure of Y-50 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.299 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A conserved human CD4+ T cell subset recognizing the mycobacterial adjuvant, trehalose monomycolate.

Sakai, Y.Asa, M.Hirose, M.Kusuhara, W.Fujiwara, N.Tamashima, H.Ikazaki, T.Oka, S.Kuraba, K.Tanaka, K.Yoshiyama, T.Nagae, M.Hoshino, Y.Motooka, D.Van Rhijn, I.Lu, X.Ishikawa, E.Moody, D.B.Kato, T.Inuki, S.Hirai, G.Yamasaki, S.

(2024) J Clin Invest 135

  • DOI: https://doi.org/10.1172/JCI185443
  • Primary Citation of Related Structures:  
    8XUB, 8ZO4, 8ZOX

  • PubMed Abstract: 

    Mycobacterium tuberculosis causes human tuberculosis. As mycobacteria are protected by thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most of these immunostimulatory lipids are known as adjuvants acting through innate immune receptors, such as C-type lectin receptors. Although a few mycobacterial lipid antigens activate unconventional T cells, antigenicity of most adjuvantic lipids are unknown. Here, we identified that trehalose monomycolate (TMM), an abundant mycobacterial adjuvant, activates human T cells bearing a unique ɑβTCR. This recognition was restricted by CD1b, a monomorphic antigen-presenting molecule conserved in primates but not mice. Single-cell TCR-RNA sequencing using newly established CD1b-TMM tetramers revealed that TMM-specific T cells are present as CD4+ effector memory T cells in the periphery of uninfected donors, but express IFNγ, TNF and anti-mycobacterial effectors upon TMM stimulation. TMM-specific T cells are detected in cord blood and PBMCs of non-BCG-vaccinated donors, but are expanded in active tuberculosis patients. A cryo-electron microscopy study of CD1b-TMM-TCR complexes revealed unique antigen recognition by conserved features of TCRs, positively-charged CDR3ɑ and long CDR3β regions. These results indicate that humans have a commonly-shared and pre-formed CD4+ T cell subset recognizing a typical mycobacterial adjuvant as an antigen. Furthermore, the dual role of TMM justifies reconsideration of the mechanism of action of adjuvants.


  • Organizational Affiliation
    • Department of Molecular Immunology, Research Institute for Microbial Diseas, Osaka University, Suita, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Y-50 alpha
A, C, E, G
205Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Y-50 beta
B, D, F, H
249Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
N [auth D]
P [auth E]
Q [auth E]
I [auth A],
K [auth B],
N [auth D],
P [auth E],
Q [auth E],
S [auth F],
T [auth G],
V [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
M [auth C]
O [auth D]
R [auth E]
J [auth A],
L [auth B],
M [auth C],
O [auth D],
R [auth E],
U [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.299 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.113α = 90
b = 168.692β = 90
c = 173.116γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23H00403
Japan Society for the Promotion of Science (JSPS)Japan22A304

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Database references
  • Version 1.2: 2025-03-26
    Changes: Database references