Nuclear pore complex and Ran-dependent karyopherin transport

Proteins and RNAs cross the nuclear envelope through nuclear pore complexes, built from nucleoporins that form a scaffold of stacked rings and a central channel lined with FG repeats. Karyopherins of the importin-beta superfamily carry cargo through the channel, and the small GTPase Ran sets the direction: Ran-GTP, made in the nucleus by RCC1, releases import cargo and loads export cargo, while Ran-GDP is returned to the nucleus by NTF2. This module is the eukaryote-wide part of that system that can be grounded locally, written so that it can be evaluated in any genome.

Eukaryote-wide scope: PAINT places the NTF2, Nup88, Cse1 (exportin-2) and Crm1-specific exportin-1 nodes at Eukaryota (taxon:2759); the Seh1/Sec13 outer-ring node and the exportin-1/5 receptor node carry no taxon in the source rows, and their seeds are listed on each node. The Ran and Nup98 families have no PAINT table locally and their selectors rest on family membership. Each cited node is shown to be an ancestor of the human protein by its IBA rows or its IBD seeds (for Cse1, which has no gene folder, by its IBA rows in QuickGO). Read as a satisfiability rule, every part is expected in any eukaryote. Molecular functions come from the human NUP98 review and from the F IBD of the exportin nodes (nuclear export signal receptor activity for both; the Cse1 node records the loss of the import-receptor activity it would otherwise inherit); Ran, NTF2, Nup88, Seh1 and Sec13 are untyped. This is a partial rule. Many required parts of the system have no local PANTHER entry for the human protein, so they cannot be family selectors in this rule: importin beta (KPNB1) and importin alpha, RCC1, RanGAP and RanBP1, and most scaffold and FG nucleoporins (NUP93, NUP205, NUP155, NUP160, NUP107, NUP85, NUP62 and others). The importins, RCC1, RanGAP1 and RanBP1 are modelled in karyopherin_nuclear_protein_import, grounded on UniProt accessions and literature rather than PANTHER families; that module also types human RAN as GTPase activity, while the Ran step here stays untyped because its family has no PAINT table or family review locally. A genome that passes this rule has therefore not been shown to have a complete pore. Selector caveats are on each family: Seh1 and Sec13 also work outside the pore, the NTF2 family takes in NXT1/NXT2, and no Dictyostelium member is listed for Nup88 or Seh1 and no Arabidopsis member for Sec13. The modules dmel_nuclear_pore_complex (Drosophila) and mrna_nuclear_export (human) describe the pore and mRNA export in one species, and karyopherin_nuclear_protein_import describes the import cycle.