4ELK

Crystal structure of the Hy19.3 type II NKT TCR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


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


Literature

Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.

Girardi, E., Maricic, I., Wang, J., Mac, T.T., Iyer, P., Kumar, V., Zajonc, D.M.

(2012) Nat Immunol 13: 851-856

  • DOI: https://doi.org/10.1038/ni.2371
  • Primary Citation of Related Structures:  
    4ELK, 4ELM

  • PubMed Abstract: 

    Glycolipids presented by the major histocompatibility complex (MHC) class I homolog CD1d are recognized by natural killer T cells (NKT cells) characterized by either a semi-invariant T cell antigen receptor (TCR) repertoire (type I NKT cells or iNKT cells) or a relatively variable TCR repertoire (type II NKT cells). Here we describe the structure of a type II NKT cell TCR in complex with CD1d-lysosulfatide. Both TCR α-chains and TCR β-chains made contact with the CD1d molecule with a diagonal footprint, typical of MHC-TCR interactions, whereas the antigen was recognized exclusively with a single TCR chain, similar to the iNKT cell TCR. Type II NKT cell TCRs, therefore, recognize CD1d-sulfatide complexes by a distinct recognition mechanism characterized by the TCR-binding features of both iNKT cells and conventional peptide-reactive T cells.

    • Organizational Affiliation: 

    Division of Cell Biology, La Jolla Institute for Allergy & Immunology, La Jolla, California, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)
A, C
208Mus musculusMutation(s): 0 
Gene Names: Valpha1 (mouse variable domain, human constant domain)
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hy19.3 TCR beta chain (mouse variable domain, human constant domain)
B, D
244Mus musculusMutation(s): 0 
Gene Names: Vbeta16 (mouse variable domain, human constant domain)
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI
Download Ideal Coordinates CCD File 
I [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
ACT
Query on ACT
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A],
J [auth B],
K [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT
Download Ideal Coordinates CCD File 
G [auth A]
L [auth B]
M [auth B]
N [auth B]
O [auth C]
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.22α = 90
b = 101.53β = 90
c = 134.49γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description