Nuclear Pore Complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here we provide a composite multiscale structure of the yeast NPC based on improved 3D density maps from electron cryo-microscopy and AlphaFold2 atomic models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals a common architecture that may be shared with ancestral NPCs. Additional connections between the scaffold and the central transporter suggest that, under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the core scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport and NPC evolution.