Fig. 4: Sso1 is threaded through the D1 and D2 domains.

a, y20S class 1 atomic model emphasizing the position of Sso1. Stars represent the crosslink identified by XL-MS (Fig. 1b). b, Bottom view of y20S class 1 D1 ring; the Habc domain is packed against the D2 ring surface, between protrusions corresponding to the C-terminal helical regions of two D2 small subdomains. All surfaces are colored gray, except for protomers A and B, which are colored by their electrostatic potential c, Rotated view of y20S class 1 relative to b showing the Habc tucked between protomers A and B, with the Habc domain colored by its electrostatic potential d, Composite cryo-EM map (blue, RELION unsharpened map: Habc domain and D1 density; cryoSPARC 3DFlex map: D2 density) of y20S class 1. e, Cryo-EM maps of all eight y20S classes reveal the Habc domain associated with the Sec18 D2 ring in all classes (red). In six of eight classes, the Habc density is radially averaged into multiple discrete positions around the D2 ring, leading to more diffuse density.