Structural basis of nectin-1 recognition by pseudorabies virus glycoprotein D
Fig 5
The atomic interaction details at the PRV-gD/SW-nectin-1 interface.
(A) An overview of the binding interface. The nectin-1 receptor is shown in surface and the gD ligand is presented as ribbons. The interface components in PRV gD, including the N-loop, the α1' helix in the IgV-like core, and the α2', α3', α3 helices and the α3'/α3 intervening loop in the C-terminal extension, are highlighted and marked with patch numbers 1–3. The amino acid interaction details for each of the three patches were delineated in panels (B), (C), and (D), respectively. (B) The interaction of the gD N-loop with nectin-1. (C) The interaction of the gD α1' and α2' helices with nectin-1. (D) The interaction of the gD α3', α3 helices and their intervening loop with nectin-1. The residues referred to in the text are shown and labeled. Dark dashed lines indicate strong H-bonds (<3.0 Å), while orange ones represent weak H-bonds (3.0–3.5 Å). (E) Amino acid sequence alignment between HU- and SW-nectin-1 highlighting their IgV domains that are recognized by PRV gD. The residues interfacing with gD are marked with black stars. For clarity, only those that contribute >2 inter-molecule Van der Waals contacts were selected. A full list of the interface residues were summarized in Table 2.