Natural killer T (NKT) cells provide an innate-type immune response upon T cell receptor interaction withCD1d-presented antigens. We demonstrate through equilibrium tetramer binding and antigen presentation assays with V␣14i-positive NKT cell hybridomas that the Sphingomonas glycolipid ␣-galacturonosyl ceramide (GalA-GSL) is a NKT cell agonist that is significantly weaker than ␣-galactosylceramide (␣-GalCer), the most potent known NKT agonist. For GalA-GSL, a shorter fatty acyl chain, an absence of the 4-OH on the sphingosine tail and a 6 -COOH group on the galactose moiety account for its observed antigenic potency. We further determined the crystal structure of mCD1d in complex with GalA-GSL at 1.8-Å resolution. The overall binding mode of GalA-GSL to mCD1d is similar to that of the short-chain ␣-GalCer ligand PBS-25, but its sphinganine chain is more deeply inserted into the F pocket due to alternate hydrogen-bonding interactions between the sphinganine 3-OH with Asp-80. Subsequently, a slight lateral shift (>1 Å) of the galacturonosyl head group is noted at the CD1 surface compared with the galactose of ␣-GalCer. Because the relatively short C 14 fatty acid of GalA-GSL does not fully occupy the A pocket, a spacer lipid is found that stabilizes this pocket. The lipid spacer was identified by GC͞MS as a mixture of saturated and monounsaturated palmitic acid (C 16). Comparison of available crystal structures of ␣-anomeric glycosphingolipids now sheds light on the structural basis of their differential antigenic potency and has led to the design and synthesis of NKT cell agonists with enhanced cell-based stimulatory activities compared with ␣-GalCer.adjuvant ͉ glycolipid T he CD1 family of antigen-presenting glycoproteins mediates T cell responses through the presentation of self and foreign lipids, glycolipids, lipopeptides, or amphipathic small molecules to T cell receptors (TCR) (1-10). In humans, the various CD1 isoforms are categorized into group I (CD1a, CD1b, CD1c, and CD1e) and group II (CD1d) based on sequence similarity (11). Through the binding and presentation of endogenous and exogenous lipid antigens to TCRs, the CD1 pathway is reminiscent of peptide presentation by MHC class I and class II molecules.The group II isotype, CD1d, presents antigens to a unique population of T lymphocytes termed natural killer T (NKT) cells (4), which express an invariant V␣14i TCR in mice or V␣24i TCR in humans, in addition to NK 1.1 and other receptors typical of NK cells (12). These cells are sometimes called V␣14i or V␣24i NKT cells to distinguish them from other T lymphocytes that can express NK1.1. The first defined and most potent V␣14i NKT cell agonist, ␣-galactosylceramide (␣-GalCer), was originally isolated from a marine sponge and subsequently optimized by medicinal chemistry (13). When bound to CD1d, ␣-GalCer strongly activates V␣14i NKT cells, causing a rapid release of T helper type 1 and 2 cytokines. Although ␣-GalCer has been of great value and use in exploration of NKT cell biology, its unusual origin ...