Killer cell immunoglobulin-like receptors (KIRs) are important receptors for regulating the killing of virus-infected or cancer cells of natural killer (NK) cells. KIR2DS2 can recognize peptides derived from hepatitis C virus (HCV) or global flaviviruses (such as dengue and Zika) presented by HLA-C*0102 to activate NK cells, and has shown promising results when used for cancer immunotherapy. Here, we present the complex structure of KIR2DS2 with HLA-C*0102 at a resolution of 2•5Å. Our structure reveals that KIR2DS2 can bind with HLA-C*0102 and HLA-A*1101 in two different directions. Moreover, Tyr45 (in activating receptor KIR2DS2) and Phe45 (in inhibitory KIRs) distinguish the two different binding models and binding affinity between activating KIRs and inhibitory KIRs. The conserved 'AT' motif of the peptide mediates recognition and determines the peptide specificity of recognition. These structural characteristics shed light on how KIRs activate NK cells and can provide a molecular basis for immunotherapy by NK cells. K E Y W O R D S activating KIRs, immune response, KIR-HLA complex structure, NK cells, recognition mechanism F I G U R E 1 Overall structure of KIR2DS2-pHLA-C*0102 complex. (a) Cartoon representation of the KIR2DS2-pHLA-C*0102 complex with KIR2DS2 coloured yellow, HLA heavy chain coloured green, β2m coloured cyan and peptide coloured magenta. (b) Flip (A) 90° to the right. (c) shows the hinge angles of KIR2DS2 in KIR2DS2-pHLA-C*0102 complex (69°, yellow) and free (73°, blue). (d) Domain axis angles among different KIR-pHLA ternary complex structures (aligned by HLA α1α2 domain): KIR2DS2-pHLA-C*0102 (yellow), KIR2DS2-pHLA-A*1101(magenta), KIR2DL1-pHLA-C*0401 (pink), KIR2DL2-pHLA-C*0304 (orange) and KIR2DS2 free (blue). The 16•9° axis angle for the D1 domain between KIR2DS2-pHLA-C*0102 and KIR2DS2-pHLA-A*1101 is indicated F I G U R E 2 Loops of KIR2DS2 adopt altered conformations upon binding to pHLA-C*0102 compared with free KIR2DS2. (a) The KIR2DS2-pHLA-C*0102 was aligned to free KIR2DS2. The overall conformation of KIR2DS2 in different structures. (b) The KIR2DS2 loops change its orientation. Arrows show the moving direction of loops, and star shows the change of amino acid side chain. (c-f) Close-up view of loop 3, loop 2, loop 6, loop 5 and loop 5'. Amino acids participated in contact are shown by sticks and labelled. Yellow dotted line indicates the hydrogen bond