Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells

Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined at 2.4 Å revealing an extended ligand binding potential of the antigen groove and a substantially different conformation compared with known CD1c structures. Computational simulations exploring different occupancy states of the groove reenacted these different CD1c conformations and suggested cholesteryl esters (CE) and acylated steryl glycosides (ASG) as new ligand classes for CD1c. Confirming this, we show that binding of CE and ASG to CD1c enables the binding of human CD1c self-reactive T-cell receptors. Hence, human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors.Cluster of differentiation 1 (CD1) proteins are a family of MHC class I-like glycoproteins that present lipid antigens to T cells. CD1 restricted T cells are abundant in humans and play important roles in host defense and immune regulation. Human CD1 proteins comprise five CD1 isoforms, CD1a, CD1b, CD1c, CD1d, and CD1e, which exhibit different intracellular trafficking behaviors and ligand binding preferences (1). Structurally, the main differences between these CD1 isoforms lie in the architecture of their lipophilic ligand binding grooves. Whereas all CD1 isoforms share a highly conserved A′ channel (or pocket) for binding C18–C26 acyl chains, specialization is provided by further connecting channels (2–7). In CD1a, the A′ channel is “fused” to a wide and shallow F′ channel, enabling binding of lipopeptides such as mycobacterial didehydroxymycobactin (DDM) (8). CD1b features a unique T′ tunnel that connects A′ and F′, thereby forming a “superchannel” for accommodating very long acyl chains (e.g., mycobacterial mycolates) (2, 4). CD1d, the only isoform also conserved in rodents, exhibits a two-branched ligand binding groove with two linear channels A′ and F′ connected near the main portal into the groove, known as the F′ portal. A similar two-branched arrangement of A′ and F′ is seen in CD1e, the only CD1 isoform not expressed on the cell surface. Compared with CD1d, CD1a, and CD1b, the portal into the groove in CD1e is widely exposed, consistent with its known role in lipid transfer processes inside lysosomes (6).CD1c presents foreign- (9, 10) as well as self-lipid antigens to T cells (11). Two recent crystal structures of human CD1c revealed a two-branched design similar to that of CD1d and CD1e, with two channels A′ and F′ connecting near the groove portal. In these structures, a mycobacterial phosphomycoketide (PM) or mannosyl-β1-phosphomycoketide (MPM) occupied the A′ channel, whereas an undefined short ligand was present in the F′ channel (7, 12). The spatial arrangement of these ligands in the CD1c groove was very similar to and virtually overlapping in 3D comparisons with that of alpha-galactosylceramide (αGC) in human CD1d (Fig. S1 A and B). Because CD1c and CD1d are known to traffic to the same intracellular compartments for antigen sampling (13), these CD1c-PM and CD1c-MPM structures did not readily explain how CD1c and CD1d could functionally differentiate. Furthermore, the F′ channel in both CD1c-PM and CD1c-MPM was widely open to solvent, which was strikingly different from known structures of CD1a, CD1b, and CD1d and reminiscent of CD1e (7, 12). Based on these facts we hypothesized that human CD1c might undergo substantial conformational transformations in the F′ channel region upon binding of more optimal ligands, with relevance for T-cell receptor binding.Open in a separate windowFig. S1.Published CD1d-αGC and CD1c-MPM structures show a similar arrangement of their bound ligands in both the A′ and F′ channel. (A) Comparison of the configurations of bound ligands in CD1d-αGC (PDB ID code 1ZT4), CD1c-MPM (PDB ID code 3OV6), and CD1c-SL (PDB ID code 5C9J). (B) Ligands bound to CD1d (PDB ID code 1ZT4) (αGC; shown in yellow) and CD1c (PDB ID code 3OV6) (MPM; shown in blue, and spacer lipid shown in cyan) are superimposed and shown in two different orientations.