3D ultrastructure of the nuclear pore complex

Abstract

Nuclear pore complexes (NPCs) perforate the double-layered nuclear envelope and form the main gateway for molecular exchange between nucleus and cytoplasm of the eukaryotic cell. Because NPCs are extraordinarily complex and large, thus challenging to investigate on a molecular level, they are still rather poorly understood, despite their pivotal role in cellular homeostasis. To decipher the NPC structure at high resolution, the prerequisite to fully understand its function, a tailored approach is necessary that feeds from complimentary data, obtained at largely different spatial resolutions. The problem is further complicated by the dynamic nature of the NPC, manifested in flexible regions and dynamic components. Here we summarize the current state of these structural efforts, describe the breakthroughs of recent years, point out the existing disputes in the field, and give an outlook of what we should expect to happen in the near future.

Figure 1. Structural aspects of the NPC and scaffold models

A) Overall architecture of the NPC determined by cryo-electron tomography and shown in a cut-away view. The nuclear envelope is colored in grey, scaffolding components of the NPC depicted in shades of yellow [16]. For scale, a canonical β-propeller in 10fold magnification is shown. β-Propellers, together with various helical units, make up a large portion of the stable NPC scaffold. Fitting of crystal structures into the cryo-ET structures is unreliable due to the resolution gap. B) Composite structure of the heptameric 575 kDa Y-complex, a major scaffolding component of the NPC. The composite is generated based on individual crystal structures [18-22], modeling [31], interaction data, and EM pictures [17,39]. C) Arrangement of the Y-complexes within the NPC as suggested by the lattice model [18,20]. Two Y-complexes are related by a 2-fold symmetry axis and span the width of the NPC, with Nup133 pointing outward. Likely 8 such pairs, consistent with the 8fold rotational symmetry of the NPC, are positioned around the central transport axis of the NPC. Whether or not the two Y complexes directly bind or not is still unresolved. Lateral connection between Y-complexes most likely occurs via other components of the NPC, but this is also not determined yet. D) Alternative model for the Y-complex arrangement within the pore. 8 Y-complexes are directly connected in head-to-tail fashion and form a ring [5,24,44,46]. Some authors argue for an arrangement with 2 stacked rings [5], others for a configuration with 4 stacked rings per NPC [24,44]. Color coding: Nup133 (red), Nup84/Nup145C/Sec13 (yellow), Nup85/Seh1 (blue), Nup120 (green).