Extended Data Figure 4. The inner and outer Y-complexes have distinct conformations and engage in locally specific sets of interactions.

(a) Arrangement of the inner and outer Y-complex as seen from above. X-ray structures were filtered to 2.3 nm resolution and colored by protein. Positions of the five interfaces between Y-complexes are indicated. (b) The inner and outer copies of Nup160 assume the same normal vector with respect to the membrane and are slightly tilted to each other because of the different diameters from the central axis. (c) The hinges between the Nup107 C- and N-terminal domains as well as within the Nup133 C-terminal domain have a different conformation in the inner and outer Y-complex. In the case of the inner stem, the middle domain of Nup133 appears slightly bent inwards compared to the conformation revealed in the X-ray structure, which can be accounted for by introducing a hinge, as previously predicted based on the Nup133 structure ²⁶. (d) Zoomed-in views showing details of five interfaces (I–V). The panels on the right indicate the viewing point. (I) Sec13 of the outer vertex interfaces with the Nup107 N-terminal domain of the inner vertex ^4,10; (II) the N-terminal beta propeller of Nup133 interfaces with Nup160 of the posterior asymmetric unit in the case of both Y-complexes, forming the head-to-tail contact that facilitates ring formation ^12,14; (III) therefore, only the beta propeller of the inner copy of Nup133 is sandwiched between both Nup160s. In this case, the N-terminal alpha-helical domain extends into a larger interface with the outer Nup160 of the posterior asymmetric unit; (IV) the very C-terminus of the inner Nup133 branches out of the inner stem to form a contact with its counterpart on the outer stem. This relatively small interface is reminiscent of a crystal contact observed in the Nup133–Nup107 structure (pdb code: 3I4R)²⁶; and (V) Nups 85 and 43 of the outer vertex form an interface with the C-terminal domain of Nup107 of the inner stem. (e) The Nup107 finger domain (red) is exclusive to higher eukaryotes. While its inner copy (shown) interfaces with Nup43 and Nup85 of the outer vertex, its outer copy interfaces with the density connecting both Y-complexes (Fig. 2a, b). A phosphorylation site in the finger domain is depicted as dark red spheres. Asterisks mark structures that can be unambiguously positioned but have some uncertainty in their orientation, that is Nup85-CTD. (f) Vertex region of the CR as seen from the central channel. Phosphorylation sites are represented as in (e). The density connecting both Y-complexes is segmented as in Fig. 2b and is in close contact with several phosphorylation sites in Sec13, Nup96 and Nup107. Phosphorylation sites in Seh1 and Nup85 are in direct proximity to the Nup214 complex region.