Natural Killer cell function is mediated by paired activating and inhibitory Killer cell Immunoglobulin-like Receptor (KIR) binding to their cognate ligands. Currently, while inhibitory KIRs and HLA interactions have been well-defined, activating members of the KIR family receptors have poorly described ligands and functions. Recent reports have highlighted that the interaction between KIR2Ds and HLA-C can be modulated by bound peptides. However, the structural bases underpinning these observations are unknown.Here, we address this by determining the crystal structures of ten KIR2DS-peptide-HLA-C ternary complexes. This structural information, coupled with extensive binding studies provide a detailed molecular portrait of KIR2DS1, KIR2DS2 and KIR2DS4 specificity and cross-reactivity towards diverse HLA-C-peptide ligands.
Our structural data revealed two distinct molecular mechanisms underpinning KIR2DS reactivity, one of which essentially overrides canonical HLA-C1/C2 group specificity that has characterised KIR2D recognition of HLA-C. While both mechanisms are acutely peptide dependent, the canonical mechanism that discriminates across HLA-C1/C2 allotypes largely mirrors that of inhibitory KIR with the exception of the presence of “spoiler” residues that both decrease their overall affinity for HLA-C and increase their peptide selectivity. On the other hand, peptides harbouring a P8-Trp were recognised by a distinct “ball-and socket” interaction that perturbed the KIRD2S-HLA-C interface, resulting in altered canonical HLA-C1/C2 group specificity. Critically we have identified a second mechanism in which the presence of select peptides contribute to HLA allomorph cross-recognition by enabling partial or complete disengagement of KIR2DS-HLA-C group specific interactions.