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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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-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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
A, C
208Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
B, D
245Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • 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  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary