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NPCAtlas

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NPCAltas

ERC Nuclear Pore Complexes (NPCs) are large macromolecular assemblies that facilitate the exchange of macromolecules between cytoplasm and nucleus of all eukaryotic cells. NPCAtlas is a research project funded by the European Research Council (ERC) that aims to elucidate how the structure of the human nuclear pore complex (NPC) is altered in a cell-type specific context. Structure determination of huge macromolecular assemblies such as the NPCs requires the integration of various types experimental data. NPCAtlas aims to facilitate data integration efforts. As a part of this project, we attempt to comprehensively link all relevant information into this webpage. Please do not hesitate to contact us if you feel that certain information is missing.

NPC composition

The inventory of all nucleoporins, the protein components of the NPC, has been (for the most part) established by systematic proteomic studies (Rout et al., 2000, Cronshaw et al., 2002). Several additional components were identified by low throughput studies. Nucleoporins, are organized in a modular way: The contain repetitive domain folds and assemble into subcomplexes, which in turn join each other in multiple copies in order to form NPCs. Although the mean residence time of nucleoporins at the NPC varies (Rabut et al., 2004) and additional proteins are often stably associated with NPCs, the following 32 human proteins are commonly defined as nucleoporins.

Nup107 subcomplex Nup160 Q12769 Nup133 Q8WUM0 Nup107 P57740 Nup96 P52948 Nup85 Q9BW27
Nup43 Q8NFH3 Nup37 Q8NFH4 Seh1 Q96EE3 Sec13 P55735 ELYS Q8WYP5
Nup93 subcomplex Nup205 Q92621 Nup188 Q5SRE5 Nup155 O75694 Nup93 Q8N1F7 Nup35 Q8NFH5
Nup62 subcomplex Nup62 P37198 Nup58 Q9VDV3 Nup54 P70582
Cytoplasmic Nup358 P49792 Nup214 P35658 Nup98 P52948 Nup88 Q9NRG9 Aladin Q9NRG9
Gle1 Q53GS7 hCG1 O15504 Rae1 P78406
Nucleoplasmic Nup153 P49790 Nup50 Q9UKX7 Tpr P12270
Transmembrane Ndc1 Q9BTX1 Pom121A Q96HA1 Pom121C A8CG34 gp210 Q8TEM1
(Nup98 and Nup96 are translated as only one protein precursor; two isoforms exist of Pom121; although some subcomplexes were biochemically well-defined, the classification above is to some extent arbitrary)

NPC stoichiometry

Accurate knowledge about the stoichiometry of all nucleoporins when assembled into nuclear pores is crucial for elucidating NPC structure and function.The stoichiometry of the human NPC was determined by targeted proteomics using heavy labeled reference peptdies for absolute quantification (Ori et al., 2013).

Other studies have adressed the stoichiometry of the rat (Cronshaw et al., 2002, Rabut et al., 2004) and yeast NPC (Rout et al., 2000). Cell-type specific compositional variations have been reported by a number of studies (for review see e.g. Raices and D'Angelo, 2012.).

Structural entries

A list of X-ray and NMR structures of nucleoporins is here.

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