Here we use X-ray crystallographic structure determination to define the molecular mechanism of SNX5-IncE interaction, and confirm this mechanism using mutagenesis both in vitro and in cells. When bound to SNX5, IncE adopts an elongated β-hairpin structure, with key hydrophobic residues docked into a complementary binding groove encompassing a helix-turn-helix structural extension that is unique to SNX5, SNX6, and the brain-specific homologue SNX32. A striking degree of evolutionary conservation in the IncE-binding groove suggests that IncE co-opts the SNX5-related molecules by displacing a host protein (as yet unidentified) that normally binds to this site. Our work thus provides both the first mechanistic insights into how protein hijacking is mediated by inclusion membrane proteins, and also sheds light on the functional role of the SNX5-related PX domains as scaffolds for protein complex assembly.