Simple fold composition and modular architecture of the nuclear pore complex

Abstract

The nuclear pore complex (NPC) consists of multiple copies of Ϸ30 different proteins [nucleoporins (nups)], forming a channel in the nuclear envelope that mediates macromolecular transport between the cytosol and the nucleus. With <5% of the nup residues currently available in experimentally determined structures, little is known about the detailed structure of the NPC. Here, we use a combined computational and biochemical approach to assign folds for Ϸ95% of the residues in the yeast and vertebrate nups. These fold assignments suggest an underlying simplicity in the composition and modularity in the architecture of all eukaryotic NPCs. The simplicity in NPC composition is reflected in the presence of only eight fold types, with the three most frequent folds accounting for Ϸ85% of the residues. The modularity in NPC architecture is reflected in its hierarchical and symmetrical organization that partitions the predicted nup folds into three groups: the transmembrane group containing transmembrane helices and a cadherin fold, the central scaffold group containing ␤-propeller and ␣-solenoid folds, and the peripheral FG group containing predominantly the FG repeats and the coiled-coil fold. Moreover, similarities between structures in coated vesicles and those in the NPC support our prior hypothesis for their common evolutionary origin in a progenitor protocoatomer. The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins. coated vesicle ͉ protocoatomer ͉ evolution ͉ fold assignment T he nuclear pore complex (NPC) is the only known selective gate for the passage of macromolecules across the nuclear envelope (NE) (1). The NPC is also one of the largest assemblies of defined structure in the cell, with a size of Ϸ50 MDa in yeast and up to 100 MDa in vertebrates. NPCs are common to all eukaryotes and are composed of a broadly conserved set of proteins termed nucleoporins (nups) (2) that have been fully cataloged for both yeast (3) and vertebrates (4).Structural characterization of the whole NPC has proven challenging, because of its size and flexibility. A consensus lowresolution map of the NPC has emerged based largely on electron cryomicroscopy and tomography studies (5-8). The NPC is a ring of eight identical spokes. Each spoke can be divided into almost identical cytosolic and nuclear half-spokes that each consist of Ϸ25 different nups (1). At the center of the NPC is an aqueous channel serving as the conduit for the transport of macromolecules. Macromolecular transport is regulated by the filamentous FG repeatcontaining nups that emanate from the NPC into the nucleoplasm and cytoplasm. A comparison of the vertebrate and yeast NPCs reveals that the main features of the complex are conserved (1, 2).Experimentally determined atomic structures are currently available for only seven nup fragments: Ϸ20 residues of the Nsp1 FxFG repeat region (9), ...

Nup53 Is Required for Nuclear Envelope and Nuclear Pore Complex Assembly

“…Interestingly, within the Nup53 167-300 truncation is an evolutionarily conserved RNA recognition motif (RRM) that is positioned within amino acid residues 167-252 of human Nup53 (Devos et al, 2006). The crystal structure of this RRM has recently been solved for M. musculus Nup53 (Handa et al, 2006).…”

Comparative interactomics provides evidence for functional specialization of the nuclear pore complex

“…4,5 The core scaffold of the NPC comprises the inner and outer rings that are composed almost exclusively of proteins comprised of b-propellers, a-solenoids, or an N-terminal b-propeller and C-terminal a-solenoid (b-a). 13,14 These characteristics are shared with major classes of membrane interacting proteins, such as vesicle coat proteins (COPI, COPII, clathrin and tethering complexes) and intraflagellar complexes, suggestive of a common ancestry between the endomembrane trafficking system and the NPC, a theory known as the "protocoatomer hypothesis". 8,13,14 Moreover, the overall architecture of the NPC's core scaffold appears to consist of multiple kinds of structural modules that nevertheless resemble each other, both in composition and in arrangement of fold and domain types.…”

“…13,14 These characteristics are shared with major classes of membrane interacting proteins, such as vesicle coat proteins (COPI, COPII, clathrin and tethering complexes) and intraflagellar complexes, suggestive of a common ancestry between the endomembrane trafficking system and the NPC, a theory known as the "protocoatomer hypothesis". 8,13,14 Moreover, the overall architecture of the NPC's core scaffold appears to consist of multiple kinds of structural modules that nevertheless resemble each other, both in composition and in arrangement of fold and domain types. 8,15,16 This supports the idea that the elaborate architecture of the NPC arose through repeated duplication events from a simple progenitor coating complex.…”

“…Sec 13 is also present in COPII complexes, further underscoring the evolutionary relationship between the NPC and coating complexes. 13,14 Nonetheless, what appear to be minor species-specific The approximate location messenger ribonucleprotein (mRNP) remodeling factors required for mRNA export out of the NPC is also shown. Table 1.…”

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex

“…The Nups can be categorized into two structural sub-groups. One category consists of structured Nups that anchor the NPC to the NE and act as the building blocks that give the NPC its overall structure and shape (Devos et al, 2006). Another category of Nups is located in and around the central channel of the NPC and consists of large natively unfolded domains that are rich in phenylalanine-glycine (FG)-repeat motifs (i.e., FG-domains; Denning et al, 2003).…”