Arf1-dependent COPI coat assembly at the Golgi

COPI-coated vesicles carry escaped ER-resident proteins back from the Golgi to the ER and move cargo between Golgi cisternae. A Sec7-domain exchange factor of the GBF1/Gea class activates the small GTPase Arf1 on cis-Golgi membranes, and Arf1-GTP recruits the heptameric coatomer complex as a preassembled unit. Coatomer's outer B-subcomplex (alpha, beta', epsilon) binds dilysine retrieval signals and forms the cage, and its inner F-subcomplex (beta, gamma, delta, zeta), related to the clathrin adaptor complexes, contacts Arf1 and the membrane. This module is the eukaryote-wide protein core of COPI coat assembly, written so that it can be evaluated in any genome.

Eukaryote-wide scope: the coatomer beta, gamma, delta and epsilon nodes are at Eukaryota (taxon:2759). The other nodes carry no taxon in the source rows: the Arf nodes and the GBF1 exchange-factor node have IBD seeds from plants and fungi as well as animals, but the alpha/beta' and zeta nodes have seeds only from animals and budding yeast, so for those subunits the eukaryote-wide reach rests on the family entries tables (members from yeasts, Arabidopsis and Dictyostelium), not on PAINT. Each node is shown to be an ancestor of the human protein by its IBD seeds or its IBA rows (from the gene's GOA file where the gene has a folder, otherwise from QuickGO); coatomer beta and epsilon are the two parts whose human proteins are not seeds of their nodes, so their QuickGO IBA rows are their only descent evidence. Read as a satisfiability rule, every part is expected in any eukaryote. Molecular functions come from the human gene reviews for coatomer gamma and delta, and from the node's F IBD for GBF1 and Arf1 (GTP binding rather than the ARF1 review's GTPase activity, which the Arf family review leaves unresolved family-wide); the other coatomer subunits are untyped, because neither source gives them a function. Selector caveats are on each family: the Arf family over-matches, the GBF1 subfamily lists no Dictyostelium member, and a fission-yeast IRD in the alpha/beta' family is bounded on those parts. Not modelled: the ArfGAPs that trigger uncoating (human ARFGAP1 has no local PANTHER entry), cargo receptors such as the KDEL receptor and p24 proteins, and the tethers and SNAREs that fuse COPI vesicles with the ER. The Drosophila-only module dmel_copi_coat covers the coat in one species.