Fig. 1: Residue-scale model derived from an integrative structure of the yeast NPC.

a All-atom reference structure of the yeast NPC¹¹. The scaffold structure, membrane placement, and disordered FG-Nup anchoring coordinates in our residue-scale model are all derived from this structure. The coloring scheme follows a grouping as defined in the original study¹¹. b Residue-scale scaffold structure (white), including a torus-shaped occlusion (dark gray) that mimics the nuclear membrane. GLFG-Nup anchoring sites are indicated in red, FG-Nup anchoring sites are indicated in blue, and Nsp1 anchoring sites are yellow. Note that not all anchoring sites are visible in this orientation due to the geometry of the scaffold. c A self-avoiding pseudo-random walk is used to generate missing loops in the scaffold structure (orange) and configurations of disordered FG-Nup segments (green), thus completing the residue-scale model of the yeast NPC. d Anchoring sites of individual GLFG-Nups (red), FG-Nups (blue), and Nsp1 (yellow) for a single spoke, including stoichiometry. e FG/GLFG-Nup anchoring sites (side-view), highlighting four out of eight symmetric NPC spokes. f Side-view and geometric details of the single-residue computational model of the yeast NPC, including NTRs (Kap95; blue), following the coloring scheme of (c). The folded domains in the FG-Nup meshwork (green surface structures) are the β-propellers at the N-termini of the Nup159 FG domains. See Suppl. Movie 1 for a short trajectory of the Kap and FG-Nup dynamics. g Zoom in on the amino acid details of a single Kap95 protein (blue) with binding sites (red) in the FG meshwork (green) featuring FG motifs (yellow). Not shown: the blue beads include cationic, anionic, and aromatic residues, while the green beads include all 20 residues.