Figure 5: Comparison of the binding modes between gD/nectin-1 and gD/HVEM.

(a) The nectin-1 binding site within HSV-1 gD. Nectin-1 is presented as cyan ribbon. The gD molecule is shown in a surface representation. The interface residues sterically congregate together to mainly form two surface patches, which are highlighted in magenta colour and labelled. The terminal extensions and the α3-helix that were referred to in the text are indicated. (b) Superimposition of the complex structure of gD (green) binding to nectin-1 (cyan) onto that of gD (magenta) with HVEM (orange). The well-aligned gD molecules are indicated. The N-terminal 22 residues of gD (loop 1–22), which are absent in the gD/nectin-1 structure are coloured yellow and labelled. The α3-helix of gD is also highlighted. (c) Structural alignment of the gD/nectin-1 complex with a previously reported free gD of the entire ectodomain. The gD and nectin-1 molecules are coloured green and cyan, respectively, for the complex, whereas the free gD is shown in magenta. The C-terminal loop (270–306), which is only visible in the free gD structure, is highlighted in blue.