Structural features of the Nup84 complex. (A) Comparison of protein–protein interfaces in our ensemble with crystallographically determined interfaces. Atomic structures for the Nup85-Seh1 (NCBI Protein Data Bank accession no. 3ewe; Brohawn et al., 2008), Nup145c-Sec13 (PDB accession no. 3bg0; Hsia et al., 2007), and Nup84-Nup145c (PDB accession no. 3iko; Nagy et al., 2009) interfaces are shown alongside the best recapitulation of each interface found among the 9,479 ensemble structures, in which the best interface has the lowest RMSD between the dimer in the model and a crystal structure of the same dimer. A single full Nup84 complex structure is provided for reference. (B) Secondary structure elements. Helical regions (α-solenoids) are shown in pink. Sheet regions (β-propellers) are shown in cyan. (C) Indication of the N and C termini positions. Each of the Nup84 complex proteins is graded from its N terminus (blue) to the C terminus (yellow). (D) Crystal structure coverage. Where crystal structures were used to represent components of the Nup84 complex structure, the complex is colored; where atomic comparative models were used, fragments are shown in gray. (E) The density of a representative Nup84 complex structure was fitted into our previously published NPC map (Alber et al., 2007b) based on the relative positions of each component within the map. One of eight instances of the structure in each of the two outer rings of the complex is shown.