3O9W

Recognition of a Glycolipid Antigen by the iNKT Cell TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The V{alpha}14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.

Li, Y.Girardi, E.Wang, J.Yu, E.D.Painter, G.F.Kronenberg, M.Zajonc, D.M.

(2010) J.Exp.Med. --: --

  • DOI: 10.1084/jem.20101335
  • Primary Citation of Related Structures:  3O8X

  • PubMed Abstract: 
  • Invariant natural killer T cells (iNKT cells) rapidly produce effector cytokines. In this study, we report the first crystal structures of the iNKT cell T cell receptor (TCR) bound to two natural, microbial glycolipids presented by CD1d. Binding of t ...

    Invariant natural killer T cells (iNKT cells) rapidly produce effector cytokines. In this study, we report the first crystal structures of the iNKT cell T cell receptor (TCR) bound to two natural, microbial glycolipids presented by CD1d. Binding of the TCR induced CDR3-α-dependent structural changes in the F' roof of CD1d; these changes resemble those occurring in the absence of TCR engagement when the highly potent synthetic antigen α-galactosylceramide (α-GalCer) binds CD1d. Furthermore, in the Borrelia burgdorferi α-galactosyl diacylglycerol-CD1d complex, TCR binding caused a marked repositioning of the galactose sugar into an orientation that closely resembles α-GalCer. The TCR-dependent reorientation of the sugar, together with the induced CD1d fit, may explain the weaker potency of the microbial antigens compared with α-GalCer. We propose that the TCR of iNKT cells binds with a conserved footprint onto CD1d, regardless of the bound glycolipid antigen, and that for microbial antigens this unique binding mode requires TCR-initiated conformational changes.


    Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A
285Mus musculusGene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Valpha14 chimera (Mouse variable domain, Human T-cell receptor alpha chain C region constant domain)
C
209Homo sapiensGene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Vbeta8.2 chimera (Mouse variable domain, Human T-cell receptor beta-2 chain C region constant domain)
D
241Homo sapiensGene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1O2
Query on 1O2

Download SDF File 
Download CCD File 
A
(2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate
1-oleoyl,2-palmitoyl-3-O(alpha-D-galactopyranosyl)-sn-glycerol
C43 H80 O10
JBZBYHKCRFIXBI-BNOJPGAFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TCRKd: 6200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.003α = 90.00
b = 188.368β = 90.00
c = 149.791γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-08-04 
  • Released Date: 2010-09-29 
  • Deposition Author(s): Zajonc, D.M., Li, Y.

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-06-21
    Type: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-06-28
    Type: Source and taxonomy