Integrative structure and functional anatomy of a nuclear pore complex

Abstract

Summary Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.

Evolutionary divergence of the nuclear pore complex from fungi to metazoans

“…NPC might be the perfect example to observe both these evolutionary forces acting at the same time and thus leading to a species‐specific interaction network. To support our view, two recent reports on tomography structure of NPC from Chlamydomonas reinhardtii and S. cerevisiae depict the architectural differences in the arrangement of major subcomplexes as compared to the H. sapiens NPC. Hence, it is important to elucidate the structural information of NPC in species‐specific context to fully understand its transport functions.…”

Interactions between non‐structured domains of FG‐ and non‐FG‐nucleoporins coordinate the ordered assembly of the nuclear pore complex in mitosis

“…3,22 Nup35 is a component of the Nup93 complex, which is the major structural unit of the inner ring, and interacts with Nups in the same complex (Nups93, 155, and 205) as well as other Nups (Nup98 and Ndc1) and the membrane. 3,22 Nup35 is a component of the Nup93 complex, which is the major structural unit of the inner ring, and interacts with Nups in the same complex (Nups93, 155, and 205) as well as other Nups (Nup98 and Ndc1) and the membrane.…”

Fantastic nuclear envelope herniations and where to find them

“…Molecular traffic across the NE is controlled by nuclear pore complexes (NPCs), ~100 MD protein channels in Metazoans (~50 MD in budding yeast) that are formed by concentric inner, outer and membrane ring assemblies that scaffold a central transport channel, cytosolic filaments and nuclear basket (Figure 1)[7,8]. These architectural units are themselves constructed from modular subcomplexes of proteins termed nucleoporins or nups that are assembled step-wise into the NE, with an emerging role for unstructured motifs that connect subcomplexes together to help build the NPC[8–10].…”

“…These architectural units are themselves constructed from modular subcomplexes of proteins termed nucleoporins or nups that are assembled step-wise into the NE, with an emerging role for unstructured motifs that connect subcomplexes together to help build the NPC[8–10]. There remains considerable interest in understanding the biochemical and morphological differences that define post-mitotic and interphase modes of NPC assembly[11–13].…”

“…These observations, in the context of several other studies[19,24,30–34], have contributed to a rough ordering of nup subcomplex recruitment to a nascent NPC assembly site, with a key transition point occurring at or just after INM-ONM fusion. At this critical step, the cytosolic-facing mRNA export platform is assembled alongside other cytosolic-facing nups like Nup358, which anchors two concentric outer ring “Y-complexes” together on the cytosolic side of the NPC (at least in Metazoans[35], budding yeast only have one Y-complex ring and lack Nup358[8,36]), effectively completing NPC assembly. We suggest that genetic perturbations that prevent INM-ONM fusion lead to the formation of NE herniations (Figure 2B).…”