Mapping the Nup84 complex connectivity to the NPC core. (A) Predicted secondary structure of truncated nup constructs, as described in the Fig. 1 legend, are shown on the top. Coomassie-stained SDS-PAGE of affinity-purified PrA-tagged truncated Nup84 complex nups and copurifying NPC core nups are shown in the middle. Protein bands marked by filled circles at the left side of each gel lane were identified by MS. The identity of the copurifying proteins is indicated in order below each lane (PrA-tagged nups are shown in blue, Nup84 complex copurifying nups in black, NPC core copurifying nups in red, and contaminates in orange; N = Nup, S1 = Seh1, and S13 = Sec13). Lanes corresponding to truncations that show no connection to other Nup84 complex components are shown on the right and were not used for the analysis. WT, wild type. (B) Quantification of the relative connectivity to the NPC core of the Nup84 complex truncation mutants. A bar graph showing the average relative molar ratio of the copurified NPC core nups is shown (see Materials and methods for details). Bars show the average value for each mutant, and the error bars define the upper and lower values obtained. Each bar is aligned with its corresponding gel lane in A. Proportional divisions (dashed gray lanes) were made, and a color code was assigned to each division (right) from dark blue to white (colored squares) to match the increasing degree of connectivity. n = 2. AU, arbitrary unit. (C) A heat map reflecting the key regions for the connectivity of the Nup84 complex to the NPC core. The color code defined in B was used to generate a heat map using a single Nup84 complex structure from the ensemble.