Fig. 3: Effect of Kap concentration on the FG-Nup meshwork in the NPC.

a–c Simulation snapshots of the yeast NPC a in the absence of Kap95, b with 40 Kap95 proteins, and c with 160 Kap95 proteins. d Radially-averaged distribution of the total protein density (Nup and Kap95) in the NPC at varying concentrations of Kap95. With increasing concentration, Kaps start coating the GLFG-ring, thus effectively decreasing the diameter of the low-density region in the center. e Radially-averaged FG-Nup density distribution in the NPC at varying concentrations of Kap95. f Radially-averaged Kap95 density distribution in the NPC at varying concentrations of Kap95. g Relative fractions of FG-Nup–Kap interactions by FG-Nup type. At low Kap concentrations, the Kaps primarily interact with the GLFG-Nups (red). At higher Kap concentrations, Kaps interact mainly with the other Nups (blue). The dashed lines mark the relative components of the collapsed (bottom) and extended (top) domains of Nsp1, respectively. h Kap95 crowding reduces the effective diameter of the (passive) transport channel, resulting in a high selectivity for large inert cargoes. The effective diameter of the transport channel as a function of the number of Kaps added to the NPC (black squares) and the energy barrier for (passive) translocation for particles with a radius of 1.5 nm (e.g. ubiquitin), 3.0 nm (e.g. BSA), and 4.5 nm (red circles). Energy barrier data are presented as the mean values, with error bars representing the standard deviation of measurements across the pore center, calculated from energy barrier values obtained at different axial (z) slices around the center of the pore.