Signal-mediated delivery of proteins in several intracellular trafficking pathways requires the adaptor complexes AP-1, AP-2 and AP-3. Adaptors are heterotetrameric protein complexes that serve in cargo sorting through binding to di-leucine or tyrosine-based signals present in the cytoplasmic tails of cargo proteins. Adaptors team up with cytoplasmic coat proteins to effect inclusion of cargo into transport vesicles. AP-1 associates with vesicles budding from the trans-side of the Golgi complex, and AP-2 with endocytic vesicles budding from the plasma membrane. Both AP-1 and AP-2 cooperate with clathrin, a complex of three heavy chains and three light chains, which polymerizes to form the scaffold of the coat. The AP-3 adaptor mediates selective transport to lysosomes and lysosome-related organelles and has important biological roles in organisms as diverse as humans, flies, mice and yeast. In yeast, AP-3 function is required for the ALP (alkaline phosphatase) pathway to the vacuole. Mutations in AP-3 subunits in mice result in coat color defects and bleeding disorders and, in Drosophila, result in defects in eye pigmentation. In humans, mutations in the AP-3 β3A subunit cause an inherited disorder, Hermansky–Pudlak syndrome (HPS), in which patients show deficiencies in skin and eye pigmentation and a complete lack of dense granules in platelets, resulting in impaired blood clotting.An ongoing controversy involves the identity of the coat protein(s) the AP-3 adaptor utilizes to effect vesicle formation in vivo. Drake et al. demonstrated in vitro that AP-3 and clathrin, together with ARF-GTP, can nucleate clathrin-coated buds and vesicles from synthetic liposomes 1xThe assembly of AP-3 adaptor complex-containing clathrin-coated vesicles on synthetic liposomes. Drake, M et al. Mol. Biol. Cell. 2000; 11: 3723–3736Crossref | PubMedSee all References1. Furthermore, clathrin can associate with AP-3 in vitro through a ‘clathrin box’ motif present in the mammalian β3 subunit. These observations are consistent with the notion that AP-3 and clathrin team up to mediate transport in this pathway. Intriguingly, however, there is strong evidence from yeast that AP-3 does not functionally associate with clathrin in this organism 2xFormation of AP-3 transport intermediates requires Vps41p function. Rehling, P et al. Nat. Cell Biol. 1999; 1: 346–353Crossref | PubMedSee all References, 3xVps41p function in the alkaline phosphatase pathway requires homo-oligomerization and interaction with AP-3 through two distinct domains. Darsow, T et al. Mol. Biol. Cell. 2001; 12: 37–51Crossref | PubMedSee all References. For instance, the phenotypes of clathrin and AP-3 mutants are dissimilar, and clathrin does not copurify with AP-3-coated vesicles. Instead, Rehling et al. demonstrated that mutants in the yeast VPS41 gene, one of ∼45 genes involved in Golgi-to-vacuole transport, display ALP-specific sorting defects, and that Vps41p can bind to the yeast AP-3 δ subunit in vitro 2xFormation of AP-3 transport intermediates requires Vps41p function. Rehling, P et al. Nat. Cell Biol. 1999; 1: 346–353Crossref | PubMedSee all References2. This suggests that AP-3 cooperates with Vps41p, rather than clathrin, in the formation of ALP pathway transport vesicles in yeast.Darsow et al.3xVps41p function in the alkaline phosphatase pathway requires homo-oligomerization and interaction with AP-3 through two distinct domains. Darsow, T et al. Mol. Biol. Cell. 2001; 12: 37–51Crossref | PubMedSee all References3 have now characterized novel vps41 alleles that came from a screen for additional components of the ALP pathway. These mutants show severe ALP sorting defects and defects in ALP vesicle formation but, unlike the vps41 null-allele, display a normal vacuolar morphology. This is important because Vps41p is also a component of the docking and fusion machinery at the vacuole, the C-Vps–HOPS complex. Thus, Vps41p might have two clearly separable functions. Darsow et al. further show that a conserved N-terminal domain on Vps41p mediates its binding to the AP-3 δ subunit, whereas a C-terminal region on Vps41p, containing a clathrin heavy chain repeat, mediates homo-oligomerization of Vps41p 3xVps41p function in the alkaline phosphatase pathway requires homo-oligomerization and interaction with AP-3 through two distinct domains. Darsow, T et al. Mol. Biol. Cell. 2001; 12: 37–51Crossref | PubMedSee all References3. The latter is a feature expected of a coat protein. Clearly, AP-3 has two good candidates for ‘partners’ to choose from. A definitive answer to the ‘AP-3 coat question’ will require characterization of mammalian orthologs of Vps41p, followed by a careful study of the colocalization and interactions of AP-3 with Vps41p and/or clathrin.