5L2K

Crystal structure of GEM42 TCR-CD1b-GMM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

T cell receptor recognition of CD1b presenting a mycobacterial glycolipid.

Gras, S.Van Rhijn, I.Shahine, A.Cheng, T.Y.Bhati, M.Tan, L.L.Halim, H.Tuttle, K.D.Gapin, L.Le Nours, J.Moody, D.B.Rossjohn, J.

(2016) Nat Commun 7: 13257-13257

  • DOI: 10.1038/ncomms13257
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CD1 proteins present microbial lipids to T cells. Germline-encoded mycolyl lipid-reactive (GEM) T cells with conserved αβ T cell receptors (TCRs) recognize CD1b presenting mycobacterial mycolates. As the molecular basis underpinning TCR recognition o ...

    CD1 proteins present microbial lipids to T cells. Germline-encoded mycolyl lipid-reactive (GEM) T cells with conserved αβ T cell receptors (TCRs) recognize CD1b presenting mycobacterial mycolates. As the molecular basis underpinning TCR recognition of CD1b remains unknown, here we determine the structure of a GEM TCR bound to CD1b presenting glucose-6-O-monomycolate (GMM). The GEM TCR docks centrally above CD1b, whereby the conserved TCR α-chain extensively contacts CD1b and GMM. Through mutagenesis and study of T cells from tuberculosis patients, we identify a consensus CD1b footprint of TCRs present among GEM T cells. Using both the TCR α- and β-chains as tweezers to surround and grip the glucose moiety of GMM, GEM TCRs create a highly specific mechanism for recognizing this mycobacterial glycolipid.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus and National Jewish Health, Aurora, Colorado, USA.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1b
A
300Homo sapiensMutation(s): 1 
Gene Names: CD1B
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
98Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GEM42 TCR alpha chain
D
204N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
GEM42 TCR beta chain
E
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6UL
Query on 6UL

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Download CCD File 
A
TETRACOSYL PALMITATE
C40 H80 O2
KKTAIMZGSAQXRE-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CS
Query on CS

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D
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
70E
Query on 70E

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Download CCD File 
E
6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose
C36 GLUCOSE MONOMYCOLATE, C36 GMM
C42 H82 O8
YOCZDGRJDQLKHW-GWLFWXKWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 174.998α = 90.00
b = 174.998β = 90.00
c = 170.869γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Other