Molecular architecture of the Nup84–Nup145C–Sec13 edge element in the nuclear pore complex lattice

Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y-complex and the heteromeric Nic96 complex. We demonstrated that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat and proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134 kDa complex of Nup84-Nup145C-Sec13 of the Y-complex. The heterotypic ACE1 interaction of Nup84-Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative “fence-like” NPC model. We construct a molecular model of the Y-complex and compare the architectural principles of COPII and NPC lattices.