4WW1

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.

Le Nours, J.Praveena, T.Pellicci, D.G.Gherardin, N.A.Ross, F.J.Lim, R.T.Besra, G.S.Keshipeddy, S.Richardson, S.K.Howell, A.R.Gras, S.Godfrey, D.I.Rossjohn, J.Uldrich, A.P.

(2016) Nat Commun 7: 10570-10570

  • DOI: 10.1038/ncomms10570
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crucial to Natural Killer T (NKT) cell function is the interaction between their T-cell receptor (TCR) and CD1d-antigen complex. However, the diversity of the NKT cell repertoire and the ensuing interactions with CD1d-antigen remain unclear. We descr ...

    Crucial to Natural Killer T (NKT) cell function is the interaction between their T-cell receptor (TCR) and CD1d-antigen complex. However, the diversity of the NKT cell repertoire and the ensuing interactions with CD1d-antigen remain unclear. We describe an atypical population of CD1d-α-galactosylceramide (α-GalCer)-reactive human NKT cells that differ markedly from the prototypical TRAV10-TRAJ18-TRBV25-1(+) type I NKT cell repertoire. These cells express a range of TCR α- and β-chains that show differential recognition of glycolipid antigens. Two atypical NKT TCRs (TRAV21-TRAJ8-TRBV7-8 and TRAV12-3-TRAJ27-TRBV6-5) bind orthogonally over the A'-pocket of CD1d, adopting distinct docking modes that contrast with the docking mode of all type I NKT TCR-CD1d-antigen complexes. Moreover, the interactions with α-GalCer differ between the type I and these atypical NKT TCRs. Accordingly, diverse NKT TCR repertoire usage manifests in varied docking strategies and specificities towards CD1d-α-GalCer and related antigens, thus providing far greater scope for diverse glycolipid antigen recognition.


    Organizational Affiliation

    Infection and Immunity Program &Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TCR Alpha Chain-TRAV21-TRAJ8
A
207Homo sapiensMutation(s): 0 
Gene Names: TRAV21, TRAC (TCRA)
Find proteins for A0A0B4J279 (Homo sapiens)
Go to UniProtKB:  A0A0B4J279
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TCR Beta Chain-TRBV7-8
B
243Homo sapiensMutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.110α = 90.00
b = 73.120β = 94.49
c = 65.600γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references, Derived calculations