Extended Data Fig. 5: Nup116 positioning and possible Nup188 SH3-like domain interactions.
From: In-cell architecture of the nuclear pore and snapshots of its turnover
a, New positioning of the Nup116 versus b, previously published integrative model (PDB-Dev ID: PDBDEV_00000010 from15, right). The two S. cerevisiae NPC models were superimposed such that the IRs are aligned to the same reference frame. The Nup116 position is shown either as the density assigned to Nup116 based on the Nup116 knockout structure in the CR (a) or as localization probability densities retrieved from reference15 model (b). The major structural elements of the NPC are indicated. The Nup116 connector cable in the in-cell model (a) has been taken from reference15 based on its position relatively to the IR. Blue bars represent crosslinks from Nup116 to other Nups15. For the in-cell model, the cryo-ET map is displayed; for the model from15, the localization probability densities (not an EM map) are shown instead. c, SH3-like domain (magenta ribbons and dotted frames) of Nup18828 (yellow ribbons) bridges the interactions between the inner and the outer rings. The positions of Nup188 crosslinking to Nup116 (the number of times that some Nup188 residues crosslink with more than one Nup116 residues are denoted in the labels in parenthesis), Nup100 and Nup145N are indicated in sphere representation (red spheres) and their location suggests that they link the connecting interfaces between the IR and the outer rings: NR brown dotted frame corresponds to an unassigned density, CR green dotted frame corresponds to Nup116 density, NR green dotted frame corresponds to a second Nup116 density, see Extended Data Fig. 6c.
