Structural insights into activation of antiviral NK cell responses

Abstract

Natural killer (NK) cells are key components of innate immune responses, providing surveillance against cells undergoing tumorigenesis or infection, by viruses or internal pathogens. NK cells can directly eliminate compromised cells and regulate downstream responses of the innate and acquired immune systems through the release of immune modulators (cytokines, interferons). The importance of the role NK cells play in immune defense was demonstrated originally in herpes viral infections, usually mild or localized, which become severe and life threatening in NK-deficient patients . NK cell effector functions are governed by balancing opposing signals from a diverse array of activating and inhibitory receptors. Many NK receptors occur in paired activating and inhibitory isoforms and recognize major histocompatibility complex (MHC) class I proteins with varying degrees of peptide specificity. Structural studies have made considerable inroads into understanding the molecular mechanisms employed to broadly recognize multiple MHC ligands or specific pathogen-associated antigens and the strategies employed by viruses to thwart these defenses. Although many details of NK development, signaling, and integration remain mysterious, it is clear that NK receptors are key components of a system exquisitely tuned to sense any dysregulation in MHC class I expression, or the expression of certain viral antigens, resulting in the elimination of affected cells.

Fig 1. The structure and domain organization of MHC class I proteins

The structure of HLA-B*5701 is shown, in two orthogonal views (A and B), as a ribbon representation (α-helices shown as coils and β-strands shown as arrows) with a semi-transparent rendering of the molecular surface superimposed. The α-chain is colored blue-to-red from N- to C-terminus and the light chain (β₂m) is colored dark gray. Domains are labeled. The peptide is shown in a CPK representation, with alternating residues colored purple or orange. The view in (B) looks down onto the top of the protein, the view seen from the perspective of an incoming TCR.

Fig 2. Interaction footprints for representative NK receptors on MHC class I proteins

Molecular surface representations of the class I ligand protein are shown, colored light gray for the heavy chain (α-chain) and dark gray for the light chain (β₂m); the bound antigenic peptide is shown as an orange squiggle. In the top row, the NK receptor is shown in ribbon representation, colored purple, with α-helices indicated as coils and β-strands indicated as arrows. The middle and bottom rows show the class I protein without the receptor, in two different orthogonal views. The interaction footprint of the receptor on the class I ligand is colored aqua, with the receptor domains contributing the contacts labeled in the middle and bottom rows. Contacts to the peptide are also colored aqua.

Fig 3. The KIR3DL1/HLA-B*5701 interface

(A) An overview of the complex is shown, with both class I ligand and KIR receptor shown in ribbon representations; a semi-transparent rendering of the molecular surface of KIR3DL1 is superimposed. The peptide is shown in CPK representation, colored by atom type (carbon: gray; oxygen: red; nitrogen: blue). (B) A zoomed-in view of the interface, centered on I80 in HLA-B. Only segments of the protein backbone ribbons and the side-chains of key residues [shown in licorice-stick representation, colored by atom-type as in (A) and labeled] are shown for clarity. The segment of the HLA-B heavy chain corresponding to the Bw4 epitope is colored gray. Direct contacts between Val166 in KIR3DL1 and Ile80 in HLA-B and P8 in the antigenic peptide are indicated with yellow dotted lines. The cluster of ordered water molecules in a pocket between the D1/HLA interface is shown as red spheres. (C) A model of the effect of substituting Val166 with arginine, the key 3DL1/3DS1 sequence difference. The side-chain of Arg166, placed in the least disallowed rotamer, is shown in CPK representation, colored by atom-type as in (A). The molecular surface of HLA-B*5701 is colored light gray for the platform domain, black for the peptide and red for P8 in the peptide. The steric clash is readily apparent, shown by the penetration of the Arg166 side-chain through the molecular surface.

Fig 4. Comparison of the KIR3DL1*001/HLA-B*5701 complex structure with the KIR3DL1*015/HLA-A24 model

(A) A superposition of KIR3DL1*001/HLA-B*5701 and KIR3DL1*015/HLA-A24 is shown as a ribbon representation. KIR3DL1*001 is colored by domain (D0 in light green, D1 in aqua, and D2 in dark green); HLA-B*5701 is colored light grey with bound peptide in orange; KIR3DL1*015 is colored by domain and labels are qualified by asterisks (D0* orange, D1* red, D2* blue); HLA-A24 is colored dark grey with bound peptide in yellow. (B) The footprint of KIR3DL1*001 is shown on the molecular surface of HLA-B*5701 (top figure) and the footprint of KIR3DL1*015 is shown on the molecular surface of HLA-A24 (bottom figure) as viewed looking down on the peptide binding platform. Individual domain contacts are colored as in (A) with the exception the D1-D2 loop of KIR which is colored dark blue. (C) Ribbon representations of KIR3DL1*001 and KIR3DL*015 are shown as viewed from above [rotated 90° from the position shown in (A)]. Individual domain contacts are colored as in (A).