Fig. 2: Gid12 binds both the substrate receptor Gid4 and the tip of Gid5 in the scaffolding module.

a Overall structure of Gid12-SRS. Gid12 is colored in blue, Gid4 in gold, Gid5 in magenta, Gid8 in salmon, and Gid1 in green. Dotted wedge highlights that Gid12 projects from the scaffolding module such that the substrate receptor, Gid4, is enwrapped around 305° in the complex. Closeup highlights interactions between Gid12, Gid4, and Gid5. b Gid12 forms a 7-bladed β-propeller, with its top face and central pore extensively interacting with Gid4, and edge binding Gid5. The β-propeller blades are labelled 1–7. c Gid12 structural elements, showing blades 1–7 from bottom and top faces of the β-propeller, color-coded in blue, green, hot pink, burnt orange, slate gray, khaki, and red, respectively. A meandering insertion in the 3rd blade (Ins3), indicated by the arrow, plugs the central pore from the bottom face of β-propeller (left); Insertion between the 3rd and 4th β-sheets in blade 4 (Ins4), insertion between blades 4 and 5 (Ins4-5), and insertion between blades 5 and 6 (Ins5-6) project outward from the center of the β-propeller (right). d Gid12 surface representation, colored by electrostatic surface potential. The bottom face is highly charged (red), whereas the top face, the surface of Ins3-Ins4 5-helix bundle, and central pore (see closeup), which interact with Gid4, are substantially hydrophobic (white). e Closeups of the superposition of Gid12-SRS with a prior structure without Gid12 (cyan, PDB ID: 6SWY) show that a ≈30-residue Gid5 disordered region (DR)—invisible in the published cryo-EM maps without Gid12—binds an edge of Gid12 formed by blades 1 and 7. f Closeups showing extensive interactions between Gid12, shown as blue cryo-EM density, and Gid4 shown as gold ribbon. The Gid4 β-barrel interacts with the top face of Gid12. The Gid4 3-helix bundle (3HB) interacts with Ins4-5 and Ins5-6 from Gid12.