4EI6

Structure of XV19 Valpha1-Vbeta16 Type-II Natural Killer T cell receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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This is version 1.2 of the entry. See complete history. 


Literature

Recognition of CD1d-sulfatide mediated by a type II natural killer T cell antigen receptor.

Patel, O., Pellicci, D.G., Gras, S., Sandoval-Romero, M.L., Uldrich, A.P., Mallevaey, T., Clarke, A.J., Le Nours, J., Theodossis, A., Cardell, S.L., Gapin, L., Godfrey, D.I., Rossjohn, J.

(2012) Nat Immunol 13: 857-863

  • DOI: 10.1038/ni.2372
  • Primary Citation of Related Structures:  
    4EI5, 4EI6

  • PubMed Abstract: 

    • Natural killer T cells (NKT cells) are divided into type I and type II subsets on the basis of differences in their T cell antigen receptor (TCR) repertoire and CD1d-antigen specificity. Although the mode by which type I NKT cell TCRs recognize CD1d- ...

    Natural killer T cells (NKT cells) are divided into type I and type II subsets on the basis of differences in their T cell antigen receptor (TCR) repertoire and CD1d-antigen specificity. Although the mode by which type I NKT cell TCRs recognize CD1d-antigen has been established, how type II NKT cell TCRs engage CD1d-antigen is unknown. Here we provide a basis for how a type II NKT cell TCR, XV19, recognized CD1d-sulfatide. The XV19 TCR bound orthogonally above the A' pocket of CD1d, in contrast to the parallel docking of type I NKT cell TCRs over the F' pocket of CD1d. At the XV19 TCR-CD1d-sulfatide interface, the TCRα and TCRβ chains sat centrally on CD1d, where the malleable CDR3 loops dominated interactions with CD1d-sulfatide. Accordingly, we highlight the diverse mechanisms by which NKT cell TCRs can bind CD1d and account for the distinct antigen specificity of type II NKT cells.

    Organizational Affiliation: 

    1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)A, C208Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)B, D245Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.268α = 90
b = 100.12β = 90
c = 152.668γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Database references
  • Version 1.2: 2012-09-05
    Changes: Database references