The nuclear pore complex has entered the atomic age

Abstract

Nuclear pore complexes (NPCs) perforate the nuclear envelope and represent the exclusive passageway into and out of the nucleus of the eukaryotic cell. Apart from their essential transport function, components of the NPC have important, direct roles in nuclear organization and in gene regulation. Because of its central role in cell biology, it is of considerable interest to determine the NPC structure at atomic resolution. The complexity of these large, 40-60 MDa protein assemblies has for decades limited such structural studies. More recently, exploiting the intrinsic modularity of the NPC, structural biologists are making progress toward understanding this nanomachine in molecular detail. Structures of building blocks of the stable, architectural scaffold of the NPC have been solved, and distinct models for their assembly proposed. Here we review the status of the field and lay out the challenges and the next steps toward a full understanding of the NPC at atomic resolution.

Figure 1. Overall Structure of the Nuclear Pore Complex

(A) Representative micrographs of NPCs from diverse eukaryotes and obtained by scanning electron microscopy. The distinct surface features that define cytoplasmic and nucleoplasmic face of the NPC are conserved, so are the overall dimensions in the plane of the nuclear envelope. Scale bar indicates 100nm. (B) Cryo-electron tomographic (cryo-ET) reconstruction of the human NPC. The nuclear basket structure and the cytoplasmic extensions are omitted for clarity. The central eightfold rotational symmetry is clearly visible. A comparison between cryo-ET reconstructions of NPCs from diverse species reveals substantial differences in the overall height (Elad et al., 2009).

Figure 2. Schematic Representation of the Modular Assembly of the NPC

The NPC is built from ~30 nucleoporins, organized in a small set of subcomplexes. The cartoon shows the major subcomplexes that make up the lattice-like scaffold (blue colors), the membrane-attachment (yellow), and the FG-network (grey) of the NPC. S.cerevisiae components on the left, metazoa, with specific additional components on the right. A few peripheral nups are left out for clarity. Simplified representation, connections are not to be taken literally and box sizes are not proportional to molecular weights.

Figure 3. Inventory of the NPC

Summary of the nucleoporins that make up the NPC. Domain architecture of nucleoporins from S.cerevisiae as determined by x-ray crystallography or prediction (where structural information is still lacking). Abundance and derived mass calculations are based on published Nup/NPC stoichiometries (Rout et al., 2000; Cronshaw et al., 2003). Nucleoporins specific to metazoa are italicized.

Figure 4. Structures of Nucleoporins

Comprehensive list of all representative nucleoporin structures published to date. PDB accession codes are indicated. Structures are gradient-colored red- or blue-to-white from N to C terminus. Residue information for each crystallized fragment are given below the structure. Structures are shown in the assembly state that is supported by crystallographic and biochemical evidence. Structures are from S.cerevisiae unless noted otherwise (h, human; m,mouse; r, rat). 2QX5(Jeudy and Schwartz, 2007); 2RFO(Schrader et al., 2008b); 3EWE(Brohawn et al., 2008); 3F3F(Debler et al., 2008); 3CQC(Boehmer et al., 2008) 3I4R, 3I5P, 3I5Q(Whittle and Schwartz, 2009), 3BG1(Hsia et al., 2007); 3HXR(Leksa et al., 2009); 1XKS(Berke et al., 2004); 1XIP(Weirich et al., 2004); 2OIT(Napetschnig et al., 2007); 2OSZ(Melcak et al., 2007); 1WWH(Handa et al., 2006); 1KO6(Hodel et al., 2002); 2Q5X/Y(Sun and Guo, 2008); 2BPT(Liu and Stewart, 2005); 3CH5(Schrader et al., 2008a); 3GJ3-8(Partridge and Schwartz, 2009); 1RRP(Vetter et al., 1999).

Figure 5. The Ancestral Coatomer Element ACE1

Four scaffold nucleoporins, Nic96, Nup85, Nup84, and Nup145C share a distinct 65 kDa domain also found in the COPII protein Sec31, manifesting common evolutionary ancestry between the two membrane coats. (Devos et al., 2004; Brohawn et al., 2008). (A) The structures of an “average” ACE1 protein (left) and Nic96 (right) are shown in cartoon form and colored from blue (N-terminus) to white (C-terminus). The regions corresponding to the crown, trunk, and tail modules are indicated. The “average” ACE1 protein was made for illustrative purposes by superimposing the known ACE1 protein structures crown, trunk, and tail modules separately and constructing each of the 28 helices and connecting loops in the most frequently observed position. The orientation of the modules with respect to one another is shown in the average ACE1 case to most clearly show the architecture and connectivity of the fold. The position of the crown and tail modules in Nic96 are rotated 60° and 20° respe ctively compared to the average ACE1 structure as indicated. (B) The amino acid assignment for each of the canonical 28 ACE1 helices is indicated for all structurally characterized ACE1 proteins. All numbering is from S. cerevisiae except for helices 21-28 from Nup84, which correspond the human homolog Nup107. Helices are colored according to the module to which they belong as are the labels in (A). n.d. (not determined) indicates helices that fall within regions of the proteins for which no structural information is available.

Figure 6. Assembly Models for the NPC

Three recently proposed models for the structural organization of the NPC are illustrated. The fence pole model (top row), computationally generated model (middle row), and lattice model (bottom row) are compared in their prediction of protein interactions within one Y-complex (left column), Y-complex organization within the NPC (middle column), and placement of Y-complexes relative to other NPC subcomplexes (right column). In the fence pole model, heterooctameric poles of Nup145C•Sec13 and Nup85•Seh1 observed in crystal structures organize four rings of 8 Y-complexes each. These four rings form a cylinder adjacent to the transmembrane Nups on the membrane side and layers of adaptor Nups followed by channel Nups towards the transport channel (Hsia et al., 2007; Debler et al., 2008). The computationally generated model provides localization volumes for each Nup and shows 8 Y-complexes arranged into two separate rings, one towards the nucleocytoplasmic and the other the cytoplasmic side of the NPC. The other Nups are arranged into membrane rings, inner rings, linkers between rings, and FG nucleoporins (Alber et al., 2007). The lattice model is based on structural homology of ACE1 proteins in the NPC and COPII vesicle coat (Brohawn et al., 2008). ACE1 proteins are colored by module with tails green, trunks orange, and crowns blue. A model of a single Y-complex incorporates the demonstrated specific interactions between domains of the 7 proteins. 8 Y-complexes are assumed to form a nucleoplasmic and cytoplasmic ring, which may or may not be connected by additional lattice elements such as Nic96 and Nup157/170 in an inner ring. The illustration is meant to emphasize the predicted open, lattice-like organization of the NPC structural scaffold and is not meant to imply specific interactions between complexes. While it seems likely that the NPC lattice will be composed of ACE1-containing edge elements and vertex elements made from β-propeller interactions as observed in the COPII vesicle coat, the exact nature of the vertex elements in the NPC lattice remains to be seen (Brohawn et al., 2008).