The Structure Inventory of the Nuclear Pore Complex

Abstract

The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.

Keywords: macromolecular complexes; nuclear pore complex.

Figure 1. Overview of the Nuclear Pore Complex

The NPC embedded in the double membrane surrounding the nucleus of eukaryotic cells. The experimental tomographic structure EMD-3105 [14] is decorated with the nuclear basket and cytoplasmic filaments depicted schematically. CR, cytoplasmic ring; IRC, inner ring complex; NR, nucleoplasmic ring.

Figure 2. Components of the Nuclear Pore Complex

Nucleoporins making up the NPC are listed. Nomenclature for yeast (Saccharomyces cerevisiae) and metazoa, respectively, is indicated. Nucleoporins are ordered according to the subassemblies they belong to. Major domain elements are color coded and illustrated by representative crystal structures. Cartoon length approximately represents the molecular weight of each nucleoporin. The majority of nucleoporins is built up from a small set of architectural elements. Notes: ^aA chain of Immunoglobulin (Ig) folds is predicted with certainty for the luminal portions of scPom152 and hsNup210, respectively. The exact number of Igs is unknown. ^bTMEM33 is the human homolog of scPom33, but it is not yet experimentally confirmed as a Nup.

Figure 3. Structures of Elements of the Nucleoplasmic/Cytoplasmic Rings

The Y complex is considered to be the main building block of the NR and CR. Panels a-c show different structures of the Y complex. (a) Composite crystal structure of the complete, heptameric Y complex of S. cerevisiae [33]. (b) Crystal structure of a contiguous hexameric subassembly of the Y complex, with a synthetic antibody (sAb, grey) as crystallization chaperone (PDB 4XMM) [66] (c) Composite EM structure of the human Y complex, obtained by docking crystal structures into a 23 Å cryo-ET density map (PDB 5A9Q) [14]. The three assemblies are superposed using the Nup145C element as template. Differences in the position of the three extremities of the Y shaped structure can largely be explained by the intrinsic flexibility of complex. (d–f) Three differently stacked helical elements within the Y complex. scNup145C (PDB 3JRO) (d) adopts the characteristic ACE1 fold-back architecture, shared with three other scaffold nups. spNup120 (PDB 4FHN) (e) and hsNup133 (PDB 1XKS, 3I4R) (f) each combine their helical domain with an N-terminal β-propeller domain, but are otherwise structurally distinct. Color gradient to indicate the N-to-C-terminal direction.

Figure 4. Structures of Elements of the Inner Ring Complex

The main members of the IRC have been crystallized mostly individually (a–d). (a) Composite structure of mtNup188, based on crystal structures (PDB 4KF7, 4KF8) and modeling [74]. (b) Composite structure of scNup157/170 (3I5P, 4MHC) [57,71]. (c) Crystal structure of Nic96 (PDB 2QX5, 2RFO) [70]. (d) Crystal structure of the dimerization domain of murine Nup35 (scNup53 homolog) (PDB 1WWH) [69]. (e) Crystal structure of the ct(Nsp1-Nup57-Nup49-Nic96) complex (Nic96 in red), obtained with a synthetic antibody (sAb, grey) as crystallization chaperone (PDB 5CWS) [32]. (f) Crystal structure of the metazoan Nup62-Nup58-Nup54 complex, obtained with a nanobody (grey) as crystallization chaperone (PDB 5C3L) [45]. The comparison of the Nsp1- and Nup62 complexes shows the remarkable conservation across the evolution of opisthokonts.

Figure 5. Structures of Elements of the Cytoplasmic Filaments

The structures represented in panels (a) and (b) are the most complex assemblies of the CFs known so far. (a) The trimeric sc(Nup159-Dbp5-Gle1) complex (PDB 3RRM) is an important regulatory element for mRNA export [87]. (b) The sc(Nup159-Nup82-Nup116) complex (PDB 3PBP) likely represents the anchoring element for the CF to the main NPC scaffold [85], because of the additional contacts scNup116 and its paralogs scNup100 and scNup145N can form with other nups [31,32,50]. (c, d) Ran interacts at the NPC periphery, including CF and basket and predominantly in metazoa, with elements that recognize either Ran-GDP (PDB 3GJ3–8, 3CH5) or Ran-GTP (PDB 1RRP) [–93]. All images are paired with a schematic representation of the interacting protein fragments, color-coded to match the cartoons.