4LHU

Crystal Structure of 9C2 TCR bound to CD1d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

CD1d-lipid antigen recognition by the gamma delta TCR.

Uldrich, A.P.Le Nours, J.Pellicci, D.G.Gherardin, N.A.McPherson, K.G.Lim, R.T.Patel, O.Beddoe, T.Gras, S.Rossjohn, J.Godfrey, D.I.

(2013) Nat.Immunol. 14: 1137-1145

  • DOI: 10.1038/ni.2713
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The T cell repertoire comprises αβ and γδ T cell lineages. Although it is established how αβ T cell antigen receptors (TCRs) interact with antigen presented by antigen-presenting molecules, this is unknown for γδ TCRs. We describe a population of hum ...

    The T cell repertoire comprises αβ and γδ T cell lineages. Although it is established how αβ T cell antigen receptors (TCRs) interact with antigen presented by antigen-presenting molecules, this is unknown for γδ TCRs. We describe a population of human Vδ1(+) γδ T cells that exhibit autoreactivity to CD1d and provide a molecular basis for how a γδ TCR binds CD1d-α-galactosylceramide (α-GalCer). The γδ TCR docked orthogonally, over the A' pocket of CD1d, in which the Vδ1-chain, and in particular the germ line-encoded CDR1δ loop, dominated interactions with CD1d. The TCR γ-chain sat peripherally to the interface, with the CDR3γ loop representing the principal determinant for α-GalCer specificity. Accordingly, we provide insight into how a γδ TCR binds specifically to a lipid-loaded antigen-presenting molecule.


    Organizational Affiliation

    1] Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d
A
278Homo sapiensMutation(s): 0 
Gene Names: CD1D
Find proteins for P15813 (Homo sapiens)
Go to Gene View: CD1D
Go to UniProtKB:  P15813
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo 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
9C2 TCR delta chain
D
236Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q6PJ56 (Homo sapiens)
Go to UniProtKB:  Q6PJ56
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
9C2 TCR gamma chain
G
251Homo sapiensMutation(s): 0 
Gene Names: TRGC1 (TCRGC1)
Find proteins for P0CF51 (Homo sapiens)
Go to UniProtKB:  P0CF51
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
JLS
Query on JLS

Download SDF File 
Download CCD File 
A
(15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide
PBS-44
C48 H93 N O9
QMLKBWVXCMTWOZ-WWHSRKRPSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 131.620α = 90.00
b = 152.690β = 90.00
c = 135.200γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
BUSTERrefinement
PHASERphasing
XDSdata reduction
BUSTER-TNTrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references