3RUG

Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties

Uldrich, A.P.Patel, O.Cameron, G.Pellicci, D.G.Day, E.B.Sullivan, L.C.Kyparissoudis, K.Kjer-Nielsen, L.Vivian, J.P.Cao, B.Brooks, A.G.Williams, S.J.Illarionov, P.Besra, G.S.Turner, S.J.Porcelli, S.A.McCluskey, J.Smyth, M.J.Rossjohn, J.Godfrey, D.I.

(2011) Nat.Immunol. 12: 616-623

  • DOI: 10.1038/ni.2051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the ...

    Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the antigen-presenting molecule CD1d. Here we describe a population of α-GalCer-reactive NKT cells that expressed a canonical V(α)10-J(α)50 TCR α-chain, which showed a preference for α-glucosylceramide (α-GlcCer) and bacterial α-glucuronic acid-containing glycolipid antigens. Structurally, despite very limited TCRα sequence identity, the V(α)10 TCR-CD1d-α-GlcCer complex had a docking mode similar to that of type I TCR-CD1d-α-GalCer complexes, although differences at the antigen-binding interface accounted for the altered antigen specificity. Our findings provide new insight into the structural basis and evolution of glycolipid antigen recognition and have notable implications for the scope and immunological role of glycolipid-specific T cell responses.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen-presenting glycoprotein CD1d1
A, C
302Mus musculusMutation(s): 0 
Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus)
Go to UniProtKB:  P11609
Entity ID: 2
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: 3
MoleculeChainsSequence LengthOrganismDetails
Valpha10(mouse variable domain, human constant domain)
E, G
204N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Vbeta8.1(mouse variable domain, human constant domain)
F, H
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DB6
Query on DB6

Download SDF File 
Download CCD File 
A, C
(11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide
C44 H83 N O9
WSXMIFGRYXQZQZ-IHVNXUITSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DB6Kd: 4400 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.140α = 90.00
b = 118.834β = 110.24
c = 108.125γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Blu-Icedata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release