The Functional Binding Site for the C-Type Lectin–Like Natural Killer Cell Receptor Ly49a Spans Three Domains of Its Major Histocompatibility Complex Class I Ligand

Natural killer (NK) cells express receptors that recognize major histocompatibility complex (MHC) class I molecules and regulate cytotoxicity of target cells. In this study, we demonstrate that Ly49A, a prototypical C-type lectin–like receptor expressed on mouse NK cells, requires species-specific determinants on β2-microglobulin (β2m) to recognize its mouse MHC class I ligand, H-2D^d. The involvement of β2m in the interaction between Ly49A and H-2D^d is also demonstrated by the functional effects of a β2m-specific antibody. We also define three residues in α1/α2 and α3 domains of H-2D^d that are critical for the recognition of H-2D^d on target cells by Ly49A. In the crystal structure of the Ly49A/H-2D^d complex, these residues are involved in hydrogen bonding to Ly49A in one of the two potential Ly49A binding sites on H-2D^d. These data unambiguously indicate that the functional effect of Ly49A as an MHC class I–specific NK cell receptor is mediated by binding to a concave region formed by three structural domains of H-2D^d, which partially overlaps the CD8 binding site.