4MNG

Structure of the DP10.7 TCR with CD1d-sulfatide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0058 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells.

Luoma, A.M.Castro, C.D.Mayassi, T.Bembinster, L.A.Bai, L.Picard, D.Anderson, B.Scharf, L.Kung, J.E.Sibener, L.V.Savage, P.B.Jabri, B.Bendelac, A.Adams, E.J.

(2013) Immunity 39: 1032-1042

  • DOI: 10.1016/j.immuni.2013.11.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nature of the antigens recognized by γδ T cells and their potential recognition of major histocompatibility complex (MHC)-like molecules has remained unclear. Members of the CD1 family of lipid-presenting molecules are suggested ligands for Vδ1 T ...

    The nature of the antigens recognized by γδ T cells and their potential recognition of major histocompatibility complex (MHC)-like molecules has remained unclear. Members of the CD1 family of lipid-presenting molecules are suggested ligands for Vδ1 TCR-expressing γδ T cells, the major γδ lymphocyte population in epithelial tissues. We crystallized a Vδ1 TCR in complex with CD1d and the self-lipid sulfatide, revealing the unusual recognition of CD1d by germline Vδ1 residues spanning all complementarity-determining region (CDR) loops, as well as sulfatide recognition separately encoded by nongermline CDR3δ residues. Binding and functional analysis showed that CD1d presenting self-lipids, including sulfatide, was widely recognized by gut Vδ1+ γδ T cells. These findings provide structural demonstration of MHC-like recognition of a self-lipid by γδ T cells and reveal the prevalence of lipid recognition by innate-like T cell populations.


    Organizational Affiliation

    Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Institute of Immunology, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute.,Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.,Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute.,Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute.,Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.,Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA. Electronic address: ejadams@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cd1d1 protein
A, C
281Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: CD1D, Cd1d1 (Cd1.1)
Find proteins for P15813 (Homo sapiens)
Go to Gene View: CD1D
Go to UniProtKB:  P15813
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
E, F
262Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q6PJ56 (Homo sapiens)
Go to UniProtKB:  Q6PJ56
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIS
Query on CIS

Download SDF File 
Download CCD File 
A, C
(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE
(2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL; CIS-TETRACOSENOYL SULFATIDE
C48 H91 N O11 S
ZZQWQNAZXFNSEP-JCOQVFCVSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0058 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 229.333α = 90.00
b = 229.333β = 90.00
c = 52.646γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-01
    Type: Database references
  • Version 1.2: 2017-06-14
    Type: Database references, Source and taxonomy, Structure summary