Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands

J Mol Biol. 2009 Nov 20;394(1):71-82. doi: 10.1016/j.jmb.2009.08.061. Epub 2009 Sep 2.


Natural killer T (NKT) cells are a subset of T cells that are activated by CD1d-glycolipid complexes through a semi-invariant alphabeta T cell receptor (NKT TCR). Upon activation, NKT cells secrete regulatory cytokines that are implicated in T helper cell responses. alpha-Galactosylceramide (alpha-GalCer) is a potent NKT cell agonist when presented by CD1d. Phenyl ring substitutions of the alpha-GalCer fatty acid moiety were recently found to be superior in eliciting regulatory cytokines. Crystal structures of four new mouse CD1d-lipid complexes (five structures), a new PBS-25 complex, and CD1d with an endogenous ligand, at 1.6-1.9 A resolution, reveal that the alpha-GalCer phenyl analogues impart minor structural differences to the A'-pocket, while the sphingosine and galactose moieties, important for NKT TCR recognition, remain virtually unchanged. The observed differences in cytokine-release profiles appear to be associated with increased stability of the CD1d-glycolipid complexes rather than increased affinity for the NKT TCR. Furthermore, comparison of mouse CD1d-glycolipid complexes in different crystallographic space groups reveals considerable conformational variation, particularly above the F'-pocket, the primary site of interaction with the NKT TCR. We propose that modifications of the sphingosine moiety or other substitutions that decrease alpha-GalCer flexibility would stabilize the F'-pocket. Such compounds might then increase CD1d affinity for the NKT TCR and further enhance the stimulatory and regulatory properties of alpha-GalCer derivatives.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, CD1d / chemistry
  • Antigens, CD1d / immunology*
  • Crystallography, X-Ray
  • Glycolipids / chemistry
  • Glycolipids / immunology*
  • Ligands
  • Lymphocyte Activation / immunology*
  • Mice
  • Models, Molecular
  • Natural Killer T-Cells / immunology*
  • Pliability
  • Protein Structure, Secondary
  • Static Electricity


  • Antigens, CD1d
  • Glycolipids
  • Ligands

Associated data

  • PDB/3GML
  • PDB/3GMM
  • PDB/3GMN
  • PDB/3GMO
  • PDB/3GMP
  • PDB/3GMQ
  • PDB/3GMR