Extended Data Fig. 3: Architectural model of S. cerevisiae NPC.
From: In-cell architecture of the nuclear pore and snapshots of its turnover
a, Comparison of fitted (to the S. cerevisiae NPC map from this study, depicted in grey) integrative inner ring complex models (red ribbons) from15 with 20 nm diameter difference. b, Representative integrative structural models of CR and NR Y-complex (blue ribbons) built in this work (see Methods) shown with the integrative model of P-complex (yellow ribbons) and refined IR (red ribbons) from15 fitted to the allocated density of the in-cell map (grey density) from this study. The Y-complexes are more extended as compared to reference15 version by ~40 Å. c, Representative integrative structural models of CR and NR Y-complex (blue ribbons), P-complex (yellow ribbons) and IR (red ribbons) from15 (PDB-Dev ID: PDBDEV_00000010) fitted to the S. cerevisiae NPC map (grey density) from this study, with respect to spatial reference frame from15. d, Representative integrative structural model of NR Y-complex (blue ribbons) built in this work shown together with the integrative model of the refined IR (red ribbons) from15 fitted to the allocated density of the S. cerevisiae NPC map (grey density). The localization probability densities of Mlp1, Mlp2 and Mlp1/Mlp2 ensemble from15 are displayed in orientation relative to the NR Y-complex as in15. Local mask refinement of n = 250 NPCs recovers extra densities in the NR that locate around the Nup120-Nup145C junction and the Nup107-Nup133 stem (left dark dotted frame). Most likely these densities account for parts of the basket since it resembles a filamentous structure15. It anchors to the regions of the Y-complex that crosslink to Mlp1 or Mlp215 and connects to the Nup85-Seh1 arm as proposed by the previous model15, but contrary to15, the filamentous region centres at the Y-complex vertex rather than at the Nup85 arm. On the right panel residues crosslinking to Mlp1 or Mlp215 are shown in sphere representation and coloured according to their confidence score (from15) with yellow – P < 0.01, green – P < 0.1, magenta P > 0.1. The shown residues, together with the yet unmodelled crosslink to residue 2 of Nup8515, emphasize that the highest confidence crosslinks are associated to the Y-complex, while the lowest confidence ones are associated to the IR. A second density (right dark dotted frame) remains unassigned, being proximate to residues crosslinking with Nup116, Nup100, Nup145N (see Extended Data Fig. 5c).
