8ZOX | pdb_00008zox

3D structure of Y-50 TCR-TMM-CD1b ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
T-cell surface glycoprotein CD1b280Homo sapiensMutation(s): 0 
Gene Names: CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens)
Explore P29016 
Go to UniProtKB:  P29016
PHAROS:  P29016
GTEx:  ENSG00000158485 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29016
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Y-50 TCR alphaC [auth D]205Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Y-50 TCR betaD [auth E]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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L2B (Subject of Investigation/LOI)
Query on A1L2B

Download Ideal Coordinates CCD File 
J [auth E][(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl (2R,3R)-3-oxidanyl-2-tetradecyl-octadecanoate
C38 H74 O8
AQVWXIRCPXPVPT-DGHSZEKHSA-N
6UL
Query on 6UL

Download Ideal Coordinates CCD File 
E [auth A]TETRACOSYL PALMITATE
C40 H80 O2
KKTAIMZGSAQXRE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth D],
G [auth D],
I [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
H [auth D]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.41

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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