Figure 3. Amino acid sequences of NKG2D ligands, NKG2D, and UL16.

(A) Sequence alignment of NKG2D ligands. Sequences of the α1α2-platform domains of NKG2D ligands MICA*01, MICB*02, ULBP1, ULBP2, ULBP3, ULBP4, ULBP5 and ULBP6 are included in the alignment. The alternative RAET nomenclature of ULBP proteins is indicated. Secondary structure elements as observed in the structure of MICBpf in complex with UL16 were assigned by DSSP [62] and are represented with cylinders (helices) and arrows (β-strands) below the alignment. Helices are named as described in [28]. Residues shaded in blue contact UL16 in the UL16-MICBpf complex. Residues shaded in salmon contact the salmon-colored NKG2D monomer (Figures 5A, B) in the MICA-NKG2D and ULBP3-NKG2D complex structures [26],[28]. Residues shaded in green contact the green NKG2D monomer (Figures 5A, B) in the MICA-NKG2D and ULBP3-NKG2D complex structures. Residues marked with a red triangle indicate substitutions between MICA and MICB in regions that contact UL16 in the MICBpf-UL16 complex. The ULBP5 residue boxed in cyan was recently shown to be the major determinant for diminished binding to NKG2D and UL16 [31]. Disulfide bridges and corresponding cysteines are represented with magenta lines. Gaps are indicated by (−). (B) Structural mimicry of UL16. Shown are relevant portions of the sequences of the green human NKG2D monomer [26],[28] (Figures 5A, B) and UL16. Secondary structure elements as observed in the structure of MICBpf in complex with UL16 and MICA in complex with NKG2D [26], respectively, were assigned and represented as described in panel A. The five residues marked with numbered black boxes below the sequence define the central binding motif that engages MICBpf or, in the case of NKG2D, MICA [26], in a similar manner (Figure 5C). Residues with the same number superimpose in space, although they are located in different regions in the protein sequences. Residues shaded in yellow and orange form contacts with MICA in the case of NKG2D [26] and with MICBpf in the case of UL16, respectively. NKG2D residues in red contact ULBP3 in the ULBP3-NKG2D complex [28]. Residues that augment the central binding motif, performing similar functions in the UL16-MICBpf and NKG2D-MICA complexes are marked with filled light red boxes below the sequence. An example is shown in Figure 5C. Disulfide bridges are represented with magenta lines. Hexagons mark the seven UL16 asparagine residues linked with glycans as observed in the UL16-MICBpf complex.