Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

Sarah A Nordeen,Daniel L Turman,Thomas U Schwartz

doi:10.1038/s41467-020-19885-5

Sarah A Nordeen, Daniel L Turman + Show 1 more

Open Access

https://doi.org/10.1038/s41467-020-19885-5

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Journal: Nature Communications	Publication Date: Nov 27, 2020
Citations: 32	License type: open-access

Affiliation: Massachusetts Institute of Technology

Abstract

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

Highlights

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions
Transport of soluble cargos across the nuclear envelope (NE) occurs solely through nuclear pore complexes (NPCs), massive, proteinaceous assemblies that sit in circular openings where inner and outer nuclear membranes fuse, effectively perforating the NE
Despite the NPC’s large mass (~60MDa in yeast), only about 30 different nucleoporins make up the 8-fold symmetric assembly of subcomplexes that together form the NPC5–9. These Nups can be classified into three main categories, (i) scaffold Nups that make up the stable structure of the NPC, (ii) peripheral Nups that are biased to one face of the NPC, and (iii) phenylalanine-glycine (FG) Nups that form the permeability barrier of the NPC

Summary

Introduction

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. The heptameric Nup[84] or Y complex is an essential scaffolding component of the NPC. In Saccharomyces cerevisiae, the heptameric 575 kDa Y complex comprises Nup[84], Nup[85], Nup[120], Nup[133], Nup145C, Sec[13], and Seh[112]. It can generally be described as having two short arms and a long stalk, connected in a central hub. Nup145C-Sec[13], and a C-terminal fragment of Nup[107] (the human homolog) with Nup[133] are known (Fig. 1b, c), the missing connection between the two yields a significant problem in modeling a composite Y complex structure.

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