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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wwPDB Validation 3D Report Full Report

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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 Related Structures: 
    8XUB, 8ZO4, 8ZOX

  • PubMed Abstract: 

    Mycobacterium tuberculosis causes human tuberculosis (TB). As mycobacteria are protected by a 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, the antigenicity of most adjuvantic lipids is unknown. Here, we identified that trehalose monomycolate (TMM), an abundant mycobacterial adjuvant, activated human T cells bearing a unique αβ T cell receptor (αβTCR). This recognition was restricted by CD1b, a monomorphic antigen-presenting molecule conserved in primates but not mice. Single-cell TCR-RNA-Seq using newly established CD1b-TMM tetramers revealed that TMM-specific T cells were present as CD4+ effector memory T cells in the periphery of uninfected donors but expressed IFN-γ, TNF, and anti-mycobacterial effectors upon TMM stimulation. TMM-specific T cells were detected in cord blood and PBMCs of donors without bacillus Calmette-Guérin vaccination but were expanded in patients with active TB. A cryo-electron microscopy study of CD1b-TMM-TCR complexes revealed unique antigen recognition by conserved features of TCRs, positively charged CDR3α, and long CDR3β regions. These results indicate that humans have a commonly shared and preformed 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 Diseases.

Macromolecule Content 

  • Total Structure Weight: 207.68 kDa 
  • Atom Count: 14,371 
  • Modeled Residue Count: 1,781 
  • Deposited Residue Count: 1,816 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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:|  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
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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