Structural evolution of the membrane-coating module of the nuclear pore complex

Abstract

The coatomer module of the nuclear pore complex borders the cylinder-like nuclear pore-membrane domain of the nuclear envelope. In evolution, a single coatomer module increases in size from hetero-heptamer (Saccharomyces cerevisiae) to hetero-octamer (Schizosaccharomyces pombe) to hetero-nonamer (Metazoa). Notably, the heptamer-octamer transition proceeds through the acquisition of the nucleoporin Nup37. How Nup37 contacts the heptamer remained unknown. Using recombinant nucleoporins, we show that Sp-Nup37 specifically binds the Sp-Nup120 member of the hetero-heptamer but does not bind an Sc-Nup120 homolog. To elucidate the Nup37-Nup120 interaction at the atomic level, we carried out crystallographic analyses of Sp-Nup37 alone and in a complex with an N-terminal, ∼110-kDa fragment of Sp-Nup120 comprising residues 1-950. Corroborating structural predictions, we determined that Nup37 folds into a seven-bladed β-propeller. Several disordered surface regions of the Nup37 β-propeller assume structure when bound to Sp-Nup120. The N-terminal domain of Sp-Nup120 1-950 also folds into a seven-bladed propeller with a markedly protruding 6D-7A insert and is followed by a contorted helical domain. Conspicuously, this 6D-7A insert contains an extension of 50 residues which also is highly conserved in Metazoa but is absent in Sc-Nup120. Strikingly, numerous contacts with the Nup37 β-propeller are located on this extension of the 6D-7A insert. Another contact region is situated toward the end of the helical region of Sp-Nup120 . Our findings provide information about the evolution and the assembly of the coatomer module of the nuclear pore complex.

Ring cycle for dilating and constricting the nuclear pore

“…One way for meeting the challenge to transport diverse substrates of a large size range would be to endow the nuclear pore with the ability to have its central transport channel undergo dilation and constriction. However, as has been argued elsewhere (1), diameter changes in the 30-nm range might buckle the membrane, if channel proteins were directly embedded into the membrane's lipid bilayer. It could be conjectured that evolution of the nuclear pore into the massive protein complex of over 100 MDa in vertebrates (reviewed in ref.…”

Spoke ring and anchorage of nuclear pore complex revealed by high resolution transmission electron microscopy

“…Moreover, the shape of the pore membrane has to be maintained for NPC functionality. Structural analysis of several NPC proteins uncovered strong similarities between modules of coated vesicles and the NPC membrane-coating module as well as the structural evolution of this module (Devos et al 2004;Debler et al 2008;DeGrasse et al 2009;Liu et al 2012).…”

Crystal structure of human nuclear pore complex component NUP43

“…Most of the loop residues are invisible and the length of the loop varies among Nup43 orthologs. In contrast, another loop between b1A and b1B (resi [19][20][21][22][23][24][25][26][27][28][29][30], exhibits an ordered conformation in the crystal structure. It is solvent accessible and protrudes at the bottom surface which might allow it to contact the helix region of hNup85, as implied by the cryo-EM structure of Nup107 complex (Fig.…”

“…In the past few years, the atomic structures of several eukaryotic Nup107 components have been determined [9], such as Nup133N-terminal domain [10], the Nup133 C-terminal domain in complex with Nup107 C-terminal domain [11], the Nup85-Seh1 complex [12,13], the Sec13-Nup145C heterodimer [14], the Sec13-Nup145C-Nup84 heterotrimer [15,16], Nup120 Nterminal domain [17,18], Nup37-Nup120 [19], the Nup145C-Nup120-central triskelion [20], and the intact complex only lacking Nup133 [9]. Recently, the low-resolution structure of the human Nup107 subcomplex within the NPC scaffold was also determined by Cryo-electron microscopy (Cryo-EM) [21].…”