3TYF | pdb_00003tyf

Crystal structure of a CD1d-lysophosphatidylcholine reactive iNKT TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3TYF

This is version 1.1 of the entry. See complete history

Literature

Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.

Lopez-Sagaseta, J.Sibener, L.V.Kung, J.E.Gumperz, J.Adams, E.J.

(2012) EMBO J 31: 2047-2059

  • DOI: https://doi.org/10.1038/emboj.2012.54
  • Primary Citation Related Structures: 
    3TYF, 3TZV, 3U0P

  • PubMed Abstract: 

    Invariant Natural Killer T (iNKT) cells use highly restricted αβ T cell receptors (TCRs) to probe the repertoire of lipids presented by CD1d molecules. Here, we describe our studies of lysophosphatidylcholine (LPC) presentation by human CD1d and its recognition by a native, LPC-specific iNKT TCR. Human CD1d presenting LPC adopts an altered conformation from that of CD1d presenting glycolipid antigens, with a shifted α1 helix resulting in an open A' pocket. Binding of the iNKT TCR requires a 7-Å displacement of the LPC headgroup but stabilizes the CD1d-LPC complex in a closed conformation. The iNKT TCR CDR loop footprint on CD1d-LPC is anchored by the conserved positioning of the CDR3α loop, whereas the remaining CDR loops are shifted, due in part to amino-acid differences in the CDR3β and Jβ segment used by this iNKT TCR. These findings provide insight into how lysophospholipids are presented by human CD1d molecules and how this complex is recognized by some, but not all, human iNKT cells.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.

Macromolecule Content 

  • Total Structure Weight: 106.39 kDa 
  • Atom Count: 6,952 
  • Modeled Residue Count: 878 
  • Deposited Residue Count: 944 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
iNKT Cell Receptor Alpha Chain
A, C
213Escherichia coliMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
iNKT Cell Receptor Beta Chain
B, D
259Escherichia coliMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth C],
K [auth C],
L [auth C],
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.602α = 103.89
b = 65.755β = 106.32
c = 66.993γ = 100.84
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary