2CDE

Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide specific T cell receptors - iNKT-TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structrue and Binding Kinetics of Three Different Human Cd1D-Alpha-Galactosylceramide-Specific T Cell Receptors

Gadola, S.D.Koch, M.Marles-Wright, J.Lissin, N.M.Sheperd, D.Matulis, G.Harlos, K.Villiger, P.M.Stuart, D.I.Jakobsen, B.K.Cerundolo, V.Jones, E.Y.

(2006) J.Exp.Med. 203: 699

  • DOI: 10.1084/jem.20052369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Invariant human TCR Valpha24-Jalpha18+/Vbeta11+ NKT cells (iNKT) are restricted by CD1d-alpha-glycosylceramides. We analyzed crystal structures and binding characteristics for an iNKT TCR plus two CD1d-alpha-GalCer-specific Vbeta11+ TCRs that use dif ...

    Invariant human TCR Valpha24-Jalpha18+/Vbeta11+ NKT cells (iNKT) are restricted by CD1d-alpha-glycosylceramides. We analyzed crystal structures and binding characteristics for an iNKT TCR plus two CD1d-alpha-GalCer-specific Vbeta11+ TCRs that use different TCR Valpha chains. The results were similar to those previously reported for MHC-peptide-specific TCRs, illustrating the versatility of the TCR platform. Docking TCR and CD1d-alpha-GalCer structures provided plausible insights into their interaction. The model supports a diagonal orientation of TCR on CD1d and suggests that complementarity determining region (CDR)3alpha, CDR3beta, and CDR1beta interact with ligands presented by CD1d, whereas CDR2beta binds to the CD1d alpha1 helix. This docking provides an explanation for the dominant usage of Vbeta11 and Vbeta8.2 chains by human and mouse iNKT cells, respectively, for recognition of CD1d-alpha-GalCer.


    Organizational Affiliation

    Department of Rheumathology and Clinical Immunology, University of Bern, Inselspital, Berne CH-3010, Switzerland. stephan.gadola@insel.ch




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INKT-TCR
A, C, E
192N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INKT-TCR
B, D, F
244Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.283 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 289.360α = 90.00
b = 84.950β = 103.30
c = 78.860γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance