AP3D1 encodes delta-adaptin, the large delta subunit of the heterotetrameric AP-3 adaptor protein complex. AP-3 (delta, a beta subunit, a mu subunit and a sigma subunit) is a cytosolic vesicle coat that is recruited to endosomal membranes by the GTP-bound form of the small GTPase ARF1, captures transmembrane cargo bearing dileucine- and tyrosine-based sorting signals, and polymerises into a tubular carrier that delivers that cargo to lysosomes and to lysosome-related organelles. Unlike the closely related AP-1 and AP-2 complexes, AP-3 does not require a clathrin lattice: its coat is built from rows of AP-3 arches cross-linked by ARF1 dimers. Within the complex, delta is the subunit that carries the primary ARF1 contact - two interfaces on its N-terminal HEAT-repeat trunk, both needed for the complex to stay on membranes - and, through a hinge in its long disordered linker, a dedicated binding site for the longin domain of the SNARE VAMP7, which AP-3 transports only when VAMP7 is engaged in a cis-SNARE complex. Delta also contributes, with the sigma subunit, to the dileucine cargo pocket. Delta is the only large subunit of AP-3 that is not duplicated in vertebrates: the ubiquitous complex uses beta-3A and the neuron-specific complex beta-3B, but both contain delta, so delta loss removes both forms. Characterised cargoes include LAMP1 and LAMP2, CD63, tyrosinase and TYRP1, VAMP7, CLN3, the zinc transporters ZnT2 and ZnT3, phosphatidylinositol-4-kinase type II alpha and, postsynaptically, AMPA receptors in complex with stargazin. Loss of delta-adaptin causes pigment-granule, platelet dense-granule, lytic-granule and synaptic-vesicle defects: it underlies the Drosophila garnet eye-colour mutant, the mouse mocha mutant, and human Hermansky-Pudlak syndrome type 10, in which oculocutaneous albinism and a platelet storage-pool defect are accompanied by neutropenia, impaired cytotoxic lymphocyte degranulation, seizures, neurodevelopmental delay and hearing loss.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000139 Golgi membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Golgi-membrane association inferred from the UniProt subcellular-location keyword. AP-3 does associate with the Golgi region, but its demonstrated mammalian budding site is the tubular sorting endosome. Reason: The UniProt SUBCELLULAR LOCATION block that seeds SL-0134 is itself flagged By similarity, and the primary human observation behind it is Simpson et al.'s anti-delta immunofluorescence, which places AP-3 at the Golgi region AND at peripheral structures. Yeast AP-3 does bud from the late Golgi, but in mammalian cells the site where AP-3 is caught budding is a tubular endosome (PMID:15051738), and the reconstituted human coat is described as an endosome-to-lysosome carrier (PMID:42139345). Keeping the location as real but peripheral to the core role. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0134 Β· Golgi apparatus membrane (UniProt subcellular location) SOURCE WEAK OR INFERRED The UniProt Golgi-membrane statement carries ECO:0000250 (By similarity), so the keyword mapping inherits an inferred source rather than a human observation. Supporting Evidence: PMID:9151686 Immunofluorescence using anti-delta antibodies reveals that the AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. |
| GO:0005515 protein binding | IPI PMID:15598649 AP-1 and AP-3 facilitate lysosomal targeting of Batten disea... | MODIFY | Summary: Bare protein binding from the CLN3 interaction. The informative statement is that AP-3 recognises a dileucine sorting signal in cargo, a site formed by the delta/sigma-3 hemicomplex. Reason: GO:0005515 records only that something was bound. The experiment is a dileucine-motif binding assay: the CLN3 dileucine motif bound AP-3 in vitro and both AP-1 and AP-3 are required for CLN3 to reach lysosomes. The 2026 coat structure locates the dileucine cargo pocket at the sigma-3/delta interface, so delta contributes directly to cargo recognition. GO:0140312 cargo adaptor activity is the informative replacement and is already used for the equivalent non-clathrin large subunit AP4E1 (IBA). The partner is CLN3/battenin (UniProtKB:Q13286, resolved via the UniProt REST record). Proposed replacements: cargo adaptor activity Supporting Evidence: PMID:15598649 The dileucine motif of CLN3 bound both AP-1 and AP-3 in vitro, and expression of mutated CLN3 in AP-1- or AP-3-deficient mouse fibroblasts showed that both adaptor complexes are required for sequential sorting of CLN3 via this motif. PMID:42139345 The known cargo binding sites on C-ΞΌ3 and Ο3/Ξ΄ are adjacent to the membrane, and the electron microscopy density suggests that they are occupied by cargo |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: AP-3 is a cytosolic coat that cycles on and off membranes; a cytoplasmic pool is exactly what is expected and what is seen when ARF1 binding is abolished. Reason: Not a throwaway location for this protein. AP-3 has low intrinsic affinity for membranes and is recruited by ARF1-GTP; when both ARF1 interfaces on delta are mutated the protein redistributes to the cytosol, which is the direct demonstration that a cytoplasmic pool exists and is the resting state. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0086 Β· Cytoplasm (UniProt subcellular location) SUPPORTS TRANSFER Keyword mapping of the UniProt Cytoplasm location; independently confirmed in human cells by the ARF1-interface mutants. Supporting Evidence: PMID:42139345 Mutations in AP3D1 that abolish interaction with ARF1 sites relocalize Ξ΄-WT-SG to the cytosol. |
| GO:0005765 lysosomal membrane | HDA PMID:17897319 Integral and associated lysosomal membrane proteins. | KEEP AS NON CORE | Summary: Detected in a placental lysosomal-membrane proteome. Plausible as a peripheral, transient association, but AP-3's productive site is the endosome upstream. Reason: A reference-projection check on PMID:17897319 (QuickGO reference= query, paginated fully) returns 242 distinct gene products, so this is a compartment survey rather than a targeted localisation claim. It is not over-annotation in the way the NK membrane proteome is, because AP-3 is genuinely an endolysosomal coat and the paper explicitly reports peripheral, lysosome-associated proteins as a category. But the compartment where AP-3 is caught doing work is the tubular sorting endosome, not the lysosomal membrane, so this is context. Supporting Evidence: PMID:17897319 Finally, our results identified a particular set of proteins with known functions in signaling and targeting to be at least partially associated with lysosomes. PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. |
| GO:0005769 early endosome | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | ACCEPT | Summary: AP-3 is on tubular domains of early/recycling endosomes; consistent with the human IDA for endosome membrane. Reason: The ComplexPortal NAS is drawn from a review whose own statement places AP-3 on early/recycling endosome tubules, and it is independently supported by direct imaging in melanocytes and by the immuno-EM that defines the AP-3 endosomal exit site. This is the compartment from which AP-3 carriers bud. Supporting Evidence: PMID:23247405 Rab32 and Rab38 interact with AP-1, AP-3 and BLOC-2 on early/recycling endosome tubules, where cargo such as tyrosinase and Tyrp1 are loaded into vesicles or transport intermediates. PMID:16162817 AP-3 and AP-1 localize in melanocytes primarily to clathrin-coated buds on tubular early endosomes near melanosomes. |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA rule ARBA00028708 firing on the AP3D1-specific CATH FunFam. True but peripheral, for the same reason as the Golgi-membrane row. Reason: I fetched ARBA00028708 from the UniProt REST ARBA endpoint and evaluated all 146 condition sets against AP3D1's full signature complement: exactly one is satisfied, 'FunFam 3.30.450.50:FF:000001 + taxon Eukaryota'. That FunFam is named 'AP-3 complex subunit delta-1, putative' in the UniProt record, so the rule is effectively AP3D1-specific rather than a fold-level over-generalisation, and the term it assigns is one Simpson et al. observed directly with an anti-delta antibody. Kept as context rather than core. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: ARBA:ARBA00028708 Β· ARBA00028708 (GO:0005794 rule) SUPPORTS TRANSFER 146 condition sets; one satisfied by AP3D1 -- FunFam 3.30.450.50:FF:000001 with taxon Eukaryota. The FunFam is the delta-1 specific one, so the rule is not fold-level over-reach. Supporting Evidence: PMID:9151686 Immunofluorescence using anti-delta antibodies reveals that the AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. |
| GO:0005794 Golgi apparatus | TAS PMID:9151686 Characterization of the adaptor-related protein complex, AP-... | KEEP AS NON CORE | Summary: The original anti-delta immunofluorescence: AP-3 at the Golgi region and at peripheral structures. Reason: This is the human primary observation, and it was made with an antibody against delta itself, so the annotation is about this gene product rather than about the complex by inference. The same paper immediately qualifies the Golgi signal by reporting peripheral structures with limited endosomal-marker overlap, and the later immuno-EM localises the budding profiles to a tubular endosome. Real location, not the core site of action. Supporting Evidence: PMID:9151686 Immunofluorescence using anti-delta antibodies reveals that the AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. PMID:9151686 These peripheral structures show only limited colocalization with endosomal markers and may correspond to a postTGN biosynthetic compartment. |
| GO:0006623 protein targeting to vacuole | IBA GO_REF:0000033 | ACCEPT | Summary: Pan-eukaryotic IBD node, seeded by the yeast APL5 experiments. Correct and core: delivering cargo to the lytic compartment is what AP-3 is for, and 'vacuole' is the compartment-agnostic parent that covers the lysosome. Reason: The IBD sits on PTN000513025 at taxon:2759 (Eukaryota) and is seeded by SGD:S000006116 = UniProtKB:Q08951, yeast APL5, which carries its own IMP for this term from PMID:17895371 (vacuolar targeting of scNcr1p perturbed in AP-3-deficient yeast). Human AP3D1 is a PTHR22781:SF12 member and so descends from that node. GO's vacuole subsumes the lysosome (GO:0006622 protein targeting to lysosome is_a GO:0006623, confirmed via the QuickGO ancestors endpoint), so nothing about the term is yeast-specific; the compartment-specific human child is added as a separate NEW row. PTHR22781 contains only AP-3 delta subunits, so this cannot be a leak from another adaptin. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000513025 Β· PTHR22781 Eukaryota (taxon:2759) IBD node PTN000513025 (seeded by yeast APL5) SUPPORTS TRANSFER Human AP3D1 is a PTHR22781:SF12 member and therefore descends from this pan-eukaryotic node; the family contains only AP-3 delta subunits (the beta subunits are PTHR11134, the alpha/gamma/epsilon subunits PTHR22780), so no AP-1/AP-2/AP-4 or beta-3 annotation can reach the target through it. SGD:S000006116 Β· yeast APL5 (UniProtKB:Q08951) SUPPORTS TRANSFER Sole gene-level donor on this row; QuickGO shows APL5 carries GO:0006623 IMP from PMID:17895371, an experimental annotation, not a propagated one. Supporting Evidence: PMID:17895371 Targeting of scNcr1p to the vacuole was perturbed in AP-3-deficient yeast cells, whereas the delivery of scNpc2p was affected by deficiencies in either AP-3 or GGA. PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. |
| GO:0006886 intracellular protein transport | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Correct but uninformative parent of everything AP-3 does. Reason: ARBA00027179 has 53 condition sets, of which AP3D1 satisfies one (bare FunFam 3.30.450.50:FF:000001, no taxon guard); InterPro IPR002553 is the adaptin-like N-terminal domain shared with AP-1/AP-2/AP-4, so this arm of the row is fold-level. The term is true - AP-3 moves proteins between intracellular compartments - but it sits far above the specific endosome-to-lysosome route that the specific rows capture. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00027179 Β· ARBA00027179 (GO:0006886 rule) SUPPORTS TRANSFER One of 53 condition sets satisfied: FunFam 3.30.450.50:FF:000001 with no taxon condition. InterPro:IPR002553 Β· IPR002553 Clathrin/coatomer adaptor, adaptin-like, N-terminal SUPPORTS TRANSFER A domain shared by the large subunits of AP-1, AP-2, AP-3 and AP-4, so it can only support a term at this level of generality. Supporting Evidence: PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. |
| GO:0006886 intracellular protein transport | TAS PMID:9151686 Characterization of the adaptor-related protein complex, AP-... | KEEP AS NON CORE | Summary: Author statement from the AP-3 characterisation paper; correct, general. Reason: Simpson et al. proposed that AP-3 works in trafficking to lysosomes or in a related pathway, which is the origin of this general transport term. It is right, and superseded in specificity by the endosome-to-lysosome and vacuole-targeting rows. Supporting Evidence: PMID:9151686 Because pigment granules are believed to be similar to lysosomes, this suggests either that the AP-3 complex may be directly involved in trafficking to lysosomes or alternatively that it may be involved in another pathway, but that missorting in that pathway may indirectly lead to defects in pigment granules. |
| GO:0006896 Golgi to vacuole transport | IBA GO_REF:0000033 | MODIFY | Summary: The yeast ALP pathway propagated to the Eukaryota node. The process transfers; the donor compartment does not - the mammalian AP-3 exit site is the tubular endosome, not the Golgi. Reason: PTN000513025 carries this term on a single gene-level donor, SGD:S000006116 (yeast APL5), whose own IMP is PMID:9335339 - the screen that defined AP-3 as the machinery carrying alkaline phosphatase and Vam3p FROM THE LATE GOLGI to the vacuole. That route is genuinely how yeast AP-3 works. In mammals it is not: immuno-EM catches AP-3 budding from a tubular endosomal compartment and AP-3-deficient cells missort LAMP-1/LAMP-2 from that compartment (PMID:15051738); in melanocytes AP-3 is on early-endosomal buds (PMID:16162817); and the reconstituted human coat is described as an endosome-to-lysosome carrier (PMID:42139345). So the biology is conserved (deliver cargo to the lytic compartment, which GO:0006623 on the same node states correctly) while the term names a compartment pair that does not transfer. Proposing GO:0008333 endosome to lysosome transport. This is a term-scoping call, not a challenge to the node: the seed is sound for yeast and the target is inside the clade. Residual uncertainty - Peden et al. call the mammalian site 'controversial' and a minor TGN pool is not excluded - is recorded in knowledge_gaps rather than resolved here. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000513025 Β· PTHR22781 Eukaryota (taxon:2759) IBD node PTN000513025 (seeded by yeast APL5) SUPPORTS SOURCE BUT NOT TARGET Node placement and clade membership are correct; what does not transfer is the Golgi donor compartment named in the term. The sibling GO:0006623 on the same node states the conserved claim without the compartment commitment. SGD:S000006116 Β· yeast APL5 (UniProtKB:Q08951) SUPPORTS SOURCE BUT NOT TARGET Sole gene-level donor; its IMP (PMID:9335339) is specifically the Golgi-to-vacuole ALP pathway, which is a yeast route. Proposed replacements: endosome to lysosome transport Supporting Evidence: PMID:9335339 A screen for factors specifically involved in transport of alkaline phosphatase (ALP) from the Golgi to the vacuole/lysosome has identified Ap16p and Ap15p of the yeast AP-3 complex. PMID:15051738 we show by immuno-electron microscopy that AP-3 is associated with budding profiles evolving from a tubular endosomal compartment that also exhibits budding profiles positive for AP-1 PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. PMID:23247405 Transport of newly synthesized tyrosinase and Tyrp1 to the maturing melanosome requires a sorting step at specialized tubular domains of early/recycling endosomes, rather than direct transport from the trans-Golgi network |
| GO:0006901 vesicle coat assembly | IEA GO_REF:0000107 | ACCEPT | Summary: AP-3 is itself a vesicle coat, and the delta subunit templates its polymerisation with ARF1. Core. Reason: The mouse donor carries this as IDA from PMID:16760431. It is now structurally explicit for the human protein: AP-3 with two bound ARF1 molecules dimerises, and the coat is built from spiralling rows of AP-3 arches linked by ARF1 dimers, with delta-ARF1-delta among the linkages modelled. Coat assembly is not a downstream consequence of AP-3 function - it is the function. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 carries GO:0006901 as IDA from PMID:16760431 (AP-3-containing vesicles generated from PC12 membranes); the claim is now independently established for the human protein by cryo-EM. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:39705307 Finally, binding of the second Arf1 molecule provides the template for AP-3 dimerization, providing a glimpse into the first step of coat polymerization. PMID:42139345 we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P2 into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers |
| GO:0007041 lysosomal transport | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Broad but correct: AP-3 moves cargo into the lysosome. Reason: ARBA00033548 has only 9 condition sets and AP3D1 satisfies one of them, 'FunFam 3.30.450.50:FF:000001 + taxon Craniata' - i.e. the AP3D1-specific FunFam with a vertebrate guard, which is a tight rule rather than a fold-level sweep. The term is a parent of the specific endosome-to-lysosome statement. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00033548 Β· ARBA00033548 (GO:0007041 rule) SUPPORTS TRANSFER One of 9 condition sets satisfied: FunFam 3.30.450.50:FF:000001 with taxon Craniata. The narrowest of the eight ARBA rules on this gene. Supporting Evidence: PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. |
| GO:0008089 anterograde axonal transport | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Neuronal context transferred from mouse, where AP-3 is needed for PI4KIIalpha to leave the cell body for neurites. Reason: Mouse Ap3d1 carries GO:0008089 as IMP from PMID:21998198: PI4KIIalpha reaches processes in wild-type neurons but not in AP-3-null or BLOC-1-null cells. The transfer is sound - delta is the shared large subunit of both AP-3A and the neuronal AP-3B, so it is present wherever the phenotype was measured - but this is the neuron-specific manifestation of AP-3's generic endosomal sorting step, not an independent axonal-transport activity of delta. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IMP for GO:0008089 from PMID:21998198; an experimental donor annotation, but one measured only in neurons. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:21998198 PI4KIIΞ± was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. PMID:17349999 Two forms of AP-3 have been characterized: a ubiquitous form, containing the Ξ΄, Ξ²3A, ΞΌ3A and Ο3(A/B) subunits, and a brain-specific form, containing Ξ²3B and ΞΌ3B in addition to the common Ξ΄ and Ο3(A/B) subunits |
| GO:0008089 anterograde axonal transport | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Curator-judged sequence-similarity transfer of the same mouse phenotype. Reason: Same donor and same underlying mouse IMP as the Ensembl-Compara row, transferred by curator judgement instead of by automatic orthology. Human and mouse delta are 1:1 orthologs in PTHR22781:SF12 and align residue-for-residue through the entire cargo-binding hinge, so there is no divergence argument against the transfer; the reservation is the same as before, that this is a neuron-specific readout. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The sole donor on this row; mouse Ap3d1 IMP from PMID:21998198. Supporting Evidence: PMID:21998198 PI4KIIΞ± was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. |
| GO:0010008 endosome membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Pan-eukaryotic node for the compartment AP-3 acts on. Core, and the target's own IDA is one of the descendant evidences behind the node. Reason: The IBD on PTN000513025 is seeded by MGI:MGI:107734 (mouse Ap3d1, IDA PMID:16162817) and by UniProtKB:O14617 - human AP3D1 itself, which carries the same IDA. The target appearing in its own WITH/FROM is the expected marker that experimental grounding exists on the target, and the IBA then adds that the localisation is inherited rather than lineage-specific. The endosomal membrane is where AP-3 is caught budding and where the reconstituted AP3:ARF1 coat forms carriers, so this is the core compartment. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Resolves to UniProtKB:O54774 (Swiss-Prot) via the UniProt xref search; carries GO:0010008 IDA from PMID:16162817. PANTHER:PTN000513025 Β· PTHR22781 Eukaryota (taxon:2759) IBD node PTN000513025 SUPPORTS TRANSFER Human AP3D1 is a PTHR22781:SF12 member and therefore descends from this pan-eukaryotic node; the family contains only AP-3 delta subunits (the beta subunits are PTHR11134, the alpha/gamma/epsilon subunits PTHR22780), so no AP-1/AP-2/AP-4 or beta-3 annotation can reach the target through it. UniProtKB:O14617 Β· human AP3D1 (the target itself) SUPPORTS TRANSFER Self-reference is correct and expected: the target's own IDA (PMID:16162817) is one of the descendant evidences the PAINT curator used to place this IBD. Not circular and not redundant. Supporting Evidence: PMID:16162817 AP-3 and AP-1 localize in melanocytes primarily to clathrin-coated buds on tubular early endosomes near melanosomes. PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. |
| GO:0010008 endosome membrane | IDA PMID:16162817 Functions of adaptor protein (AP)-3 and AP-1 in tyrosinase s... | ACCEPT | Summary: Direct imaging of AP-3 on tubular early endosomes in melanocytes. Reason: This is the human experimental anchor for the compartment, and it is the same observation that seeds the IBD node. AP-3-deficient melanocytes accumulate tyrosinase in vacuolar and multivesicular endosomes, which is the loss-of-function counterpart to the localisation. Supporting Evidence: PMID:16162817 AP-3 and AP-1 localize in melanocytes primarily to clathrin-coated buds on tubular early endosomes near melanosomes. PMID:16162817 In AP-3-deficient melanocytes, tyrosinase accumulates inappropriately in vacuolar and multivesicular endosomes. |
| GO:0010008 endosome membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Combined ARBA + Ensembl-Compara route to the same, well-supported compartment. Reason: Three independent arms agree and all are sound: ARBA00028306 fires on the AP3D1-specific FunFam with a Eukaryota guard (1 of 27 condition sets satisfied), and the Ensembl arm transfers the mouse Ap3d1 IDA from PMID:16162817. The same term is separately supported by a human IDA and by the IBA, so nothing here rests on the electronic route alone. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00028306 Β· ARBA00028306 (GO:0010008 rule) SUPPORTS TRANSFER One of 27 condition sets satisfied: FunFam 3.30.450.50:FF:000001 with taxon Eukaryota. UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0010008 from PMID:16162817. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:16162817 AP-3 and AP-1 localize in melanocytes primarily to clathrin-coated buds on tubular early endosomes near melanosomes. |
| GO:0010496 intercellular transport | IEA GO_REF:0000117 | REMOVE | Summary: 'The movement of substances between cells' - AP3D1 is a cytosolic coat subunit acting on intracellular membranes. The rule fires on a single unguarded FunFam. Reason: GO:0010496 is defined as the movement of substances between cells. Nothing in the AP-3 literature has AP3D1 transferring material from one cell to another; every characterised cargo (LAMP1/LAMP2, CD63, tyrosinase, VAMP7, ZnT2/ZnT3, PI4KIIalpha, CLN3) moves between intracellular compartments of the same cell. I fetched ARBA00092758 and evaluated all 99 condition sets against AP3D1's complete signature complement: exactly one is satisfied, a bare 'FunFam 3.30.450.50:FF:000001' with no taxon guard - the same AP3D1-specific FunFam that correctly yields 'lysosomal transport' and 'endosome membrane' under other rules. The identical evidence therefore produces a term with the wrong topology. This is the one electronic row here removed on a positive biological argument rather than for generality. Propagation Review Root cause: SOURCE BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: ARBA:ARBA00092758 Β· ARBA00092758 (GO:0010496 rule) SOURCE BAD 99 condition sets; the only one AP3D1 satisfies is an unguarded 'FunFam 3.30.450.50:FF:000001'. A delta-adaptin-specific FunFam cannot support a between-cells transport term. Supporting Evidence: PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. |
| GO:0015031 protein transport | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from the two delta-specific InterPro entries. Correct, general. Reason: Unlike the IPR002553 arm elsewhere in this record, both signatures here are delta-specific: IPR017105 is the AP-3 delta-subunit family entry and IPR010474 the metazoan delta domain. The mapping is therefore well grounded; the term is simply a high-level parent of the specific endosome-to-lysosome cargo route. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR010474 Β· IPR010474 AP-3 complex subunit delta domain, metazoa SUPPORTS TRANSFER Delta-specific and metazoan; it contains the VAMP7-binding hinge, so it is a signature of AP-3 cargo capture rather than of a generic fold. InterPro:IPR017105 Β· IPR017105 Adaptor protein complex AP-3, delta subunit SUPPORTS TRANSFER The family-level delta entry, integrated with PTHR22781; as specific a signature as this protein has. Supporting Evidence: PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: From an NK-cell membrane proteome that projects onto 1142 distinct gene products. A survey hit, not a localisation claim. Reason: Reference-projection test: querying QuickGO with reference=PMID:19946888 and paginating fully returns 1142 distinct gene products. The paper itself says roughly 40% of its identifications were predicted membrane proteins and that the remainder are things transiently associated with membranes - which is exactly what AP-3 is. The term is not false (a peripheral coat is attached to a membrane) but it carries no information about AP3D1 that the endosome-membrane rows do not carry better. Supporting Evidence: PMID:19946888 The remaining species were largely involved in cellular processes and molecular functions that could be predicted to be transiently associated with membranes. |
| GO:0016050 vesicle organization | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Parent term; AP-3 does organise vesicles, and in neurons its loss changes synaptic-vesicle size. Reason: ARBA00028845 fires on the AP3D1-specific FunFam with a Euarchontoglires guard (1 of 33 condition sets). The claim is independently true: in mouse, loss of AP-3 changes synaptic-vesicle size in a brain-region-specific way, and AP-3 is the coat that shapes its own carriers. Kept as the uninformative parent of the specific coat-assembly and SV rows. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00028845 Β· ARBA00028845 (GO:0016050 rule) SUPPORTS TRANSFER One of 33 condition sets satisfied: FunFam 3.30.450.50:FF:000001 with taxon Euarchontoglires. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:0016182 synaptic vesicle budding from endosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node seeded by mouse and rat Ap3d1, both with IDA and IMP. Delta is in the neuronal AP-3B as well as the ubiquitous AP-3A, so the term belongs on it. Reason: PTN000513028 sits at taxon:33213 (Bilateria) and carries two gene-level donors here, MGI:MGI:107734 (mouse Ap3d1, IDA+IMP PMID:11588176) and RGD:1308659 (rat Ap3d1, resolving to UniProtKB:B5DFK6, IDA+IMP PMID:22539861). Both are real experimental annotations. The subtlety the reviewer must not get wrong is that the in vitro budding activity is a property of the NEURONAL AP-3B complex - only the neuronal form makes synaptic vesicles from endosomes - but delta is the shared large subunit of both forms, so a delta annotation is correct rather than a beta-3 leak. Non-core because it is the neuronal instance of the same endosomal budding step that the coat-assembly and endosome-membrane rows state generically. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 carries GO:0016182 as both IDA and IMP from PMID:11588176. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. RGD:1308659 Β· rat Ap3d1 (UniProtKB:B5DFK6) SUPPORTS TRANSFER The UniProt xref search returns five rat Ap3d1 entries, all TrEMBL, of which B5DFK6 is the one GOA uses; QuickGO shows IDA+IMP for this term from PMID:22539861. A second, independent gene-level donor on this row -- so 'the IBD seed' would be wrong here. Supporting Evidence: PMID:11588176 However, only the neuronal form of AP-3 can produce synaptic vesicles from endosomes in vitro. PMID:17349999 Two forms of AP-3 have been characterized: a ubiquitous form, containing the Ξ΄, Ξ²3A, ΞΌ3A and Ο3(A/B) subunits, and a brain-specific form, containing Ξ²3B and ΞΌ3B in addition to the common Ξ΄ and Ο3(A/B) subunits PMID:22539861 We have identified an essential requirement for both adaptor protein complexes 1 and 3 in this process by employing morphological and optical tracking of bulk endosome-derived synaptic vesicles in rat primary neuronal cultures. |
| GO:0016182 synaptic vesicle budding from endosome | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Same mouse and rat donors by the automatic route. Reason: Four supporting entities that are two donors: UniProtKB:B5DFK6 with its Ensembl translation ENSRNOP00000025878 (rat), and UniProtKB:O54774 with ENSMUSP00000020420 (mouse). Both donors carry experimental annotations for this term. Same verdict as the IBA row - correct, and neuron-specific context rather than the core molecular role. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:B5DFK6 Β· rat Ap3d1 SUPPORTS TRANSFER Rat donor; IDA+IMP from PMID:22539861. ensembl:ENSRNOP00000025878 Β· rat Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara id for the same rat Ap3d1 as UniProtKB:B5DFK6 -- one donor under two identifiers. UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse donor; IDA+IMP from PMID:11588176. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:11588176 However, only the neuronal form of AP-3 can produce synaptic vesicles from endosomes in vitro. |
| GO:0016183 synaptic vesicle coating | NAS PMID:15537701 Genetic analysis of the neuronal and ubiquitous AP-3 adaptor... | MODIFY | Summary: The GO term means clathrin-coated pit formation at the presynaptic plasma membrane. AP-3 does not act there; the cited paper is about endosomal sorting of synaptic-vesicle proteins. Reason: GO:0016183 is defined as 'The formation of clathrin coated pits in the presynaptic membrane endocytic zone, triggered by the presence of high concentrations of synaptic vesicle components' - clathrin-mediated endocytosis at the plasma membrane. Seong et al., the cited source, report nothing of the kind: they compare beta3A- and beta3B-containing AP-3 complexes and measure the synaptic-vesicle content of ZnT3 and ClC-3, i.e. sorting into vesicles derived from endosomes. AP-3 vesicle budding is also demonstrably clathrin-independent (PMID:23761069, PMID:42139345). The process the source actually supports is GO:0016182 synaptic vesicle budding from endosome, which is proposed as the replacement (a term already on the gene by IBA - a duplicate GO id is acceptable and is preferable to leaving a mis-scoped term standing). Proposed replacements: synaptic vesicle budding from endosome Supporting Evidence: PMID:15537701 Consistently, beta3B deficiency compromised synaptic zinc stores assessed by Timm's staining and the synaptic vesicle targeting of membrane proteins involved in zinc uptake (ZnT3 and ClC-3). PMID:23761069 These findings indicate that AP-3-clathrin association is dispensable for endosomal AP-3 vesicle budding and suggest that endosomal AP-3-clathrin interactions differ from those by which AP-1 and AP-2 adaptors productively engage clathrin in vesicle biogenesis. |
| GO:0016192 vesicle-mediated transport | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Fold-level InterPro2GO mapping to a very high-level term. Reason: IPR002553 is the adaptin-like N-terminal domain shared by the large subunits of AP-1, AP-2, AP-3 and AP-4, so it can only justify a term at the level of 'vesicle-mediated transport'. True, and entirely uninformative about which vesicles or which route. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR002553 Β· IPR002553 Clathrin/coatomer adaptor, adaptin-like, N-terminal SUPPORTS TRANSFER Shared across all four adaptin large-subunit families; supports only a top-level trafficking term. Supporting Evidence: PMID:42139345 The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. |
| GO:0016192 vesicle-mediated transport | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: Complex-level author statement; correct and general. Reason: The ComplexPortal NAS records that AP-3 is part of the ubiquitous machinery that loads cargo into vesicles at endosomal tubules. Correct, but a parent of the specific rows. Supporting Evidence: PMID:23247405 Rab32 and Rab38 interact with AP-1, AP-3 and BLOC-2 on early/recycling endosome tubules, where cargo such as tyrosinase and Tyrp1 are loaded into vesicles or transport intermediates. |
| GO:0030117 membrane coat | IEA GO_REF:0000002 | ACCEPT | Summary: AP-3 is a membrane coat in the literal, structural sense: spiralling arches linked by ARF1 dimers on a tubulated membrane. Reason: The InterPro2GO route is fold-level, but the conclusion is now established directly for human AP-3 rather than inferred from the adaptin fold: cryo-ET shows AP3:ARF1 remodelling cargo-bearing membranes into tubules coated in spiralling rows of AP3 arches, and mutating the lattice interfaces breaks carrier formation in cells. Core. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR002553 Β· IPR002553 Clathrin/coatomer adaptor, adaptin-like, N-terminal SUPPORTS TRANSFER A fold-level signature, but one whose GO mapping happens to be exactly right here: the adaptin N-terminal trunk is the arch that forms the AP-3 lattice. Supporting Evidence: PMID:42139345 we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P2 into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers PMID:42139345 Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. |
| GO:0030123 AP-3 adaptor complex | IBA GO_REF:0000033 | ACCEPT | Summary: Complex membership at the Eukaryota node, seeded by yeast and Dictyostelium. The defining, core statement about this protein. Reason: PTN000513025 carries this with two gene-level donors: SGD:S000006116 (yeast APL5, IMP+IPI from PMID:9250663, the suppressor screen that showed the four yeast AP-related proteins form one high-molecular-weight complex) and dictyBase:DDB_G0279537 (UniProtKB:Q54WN0, IDA from PMID:18634783). Human delta was shown to be a subunit of the same complex in the founding papers. Note that the GO definition of this term itself records that 'AP-3 does not appear to associate with clathrin in all organisms', which is consistent with the mammalian clathrin-independence established since. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000513025 Β· PTHR22781 Eukaryota (taxon:2759) IBD node PTN000513025 (seeded by yeast APL5 and Dictyostelium ap3d1) SUPPORTS TRANSFER Human AP3D1 is a PTHR22781:SF12 member and therefore descends from this pan-eukaryotic node; the family contains only AP-3 delta subunits (the beta subunits are PTHR11134, the alpha/gamma/epsilon subunits PTHR22780), so no AP-1/AP-2/AP-4 or beta-3 annotation can reach the target through it. SGD:S000006116 Β· yeast APL5 (UniProtKB:Q08951) SUPPORTS TRANSFER IMP and IPI for this term from PMID:9250663. One of two gene-level donors on this row. dictyBase:DDB_G0279537 Β· Dictyostelium ap3d1 (UniProtKB:Q54WN0) SUPPORTS TRANSFER Single Swiss-Prot hit on the UniProt xref search; IDA for this term from PMID:18634783. Supporting Evidence: PMID:9151686 Antibodies raised against recombinant delta and sigma3 show that they are the other two subunits of the adaptor-like complex. PMID:9250663 The four yeast subunits are associated in a high-molecular-weight complex. PMID:9303295 Biochemical analyses demonstrated that delta-adaptin is a component of the adaptor-like complex AP-3 in human cells. |
| GO:0030123 AP-3 adaptor complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the two delta-specific entries; the mapping is as specific as it could be. Reason: IPR017105 is the AP-3 delta-subunit family entry (integrated with PTHR22781) and IPR010474 the metazoan delta domain. Neither is shared with another adaptin, so the complex assignment is not a fold-level guess. Independently established experimentally. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR010474 Β· IPR010474 AP-3 complex subunit delta domain, metazoa SUPPORTS TRANSFER Delta-specific metazoan domain. InterPro:IPR017105 Β· IPR017105 Adaptor protein complex AP-3, delta subunit SUPPORTS TRANSFER The delta-subunit family entry; integrated with PTHR22781, the family that contains only AP-3 delta proteins. Supporting Evidence: PMID:9303295 Biochemical analyses demonstrated that delta-adaptin is a component of the adaptor-like complex AP-3 in human cells. |
| GO:0030123 AP-3 adaptor complex | NAS PMID:9151686 Characterization of the adaptor-related protein complex, AP-... | ACCEPT | Summary: The paper that named AP-3 and identified delta as one of its four subunits, using an antibody against delta. Reason: Recorded as NAS but the paper is the primary human evidence: the p160 band that co-precipitates with mu3 and beta3 was cloned, shown to be a homolog of the alpha/gamma adaptins, and confirmed as a complex subunit with a specific antibody. This is the anchor for the whole record. Supporting Evidence: PMID:9151686 Antibodies raised against recombinant delta and sigma3 show that they are the other two subunits of the adaptor-like complex. PMID:9151686 The other two proteins that coimmunoprecipitate with ΞΌ3 and Ξ²3, p160 and p25, are labeled Ξ΄ and Ο3, respectively. |
| GO:0030424 axon | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mouse immuno-EM places most AP-3 in presynaptic axonal compartments; transferred by orthology. Reason: Mouse Ap3d1 carries GO:0030424 as IDA from PMID:20089890, where quantitative immuno-EM put the majority of AP-3 immunoreactivity in presynaptic axonal compartments of striatum and hippocampus. Sound transfer, neuron-specific context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0030424 from PMID:20089890. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:0032438 melanosome organization | IC PMID:22511774 BLOC-2, AP-3, and AP-1 proteins function in concert with Rab... | KEEP AS NON CORE | Summary: Inferred by the curator from the endosome-to-melanosome transport annotation on the same paper. Real, and cell-type specific. Reason: The IC is drawn from GO:0035646 on the same reference, and the underlying biology is among the best-established facts about AP-3 delta: garnet flies have reduced eye pigment granules, mocha mice have coat and eye colour dilution, and HPS10 patients have oculocutaneous albinism. It is kept as non-core because melanosome biogenesis is the melanocyte instance of the single generic sorting step AP-3 performs, not a separate evolved activity of delta. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: GO:0035646 Β· GO:0035646 endosome to melanosome transport (the annotation this IC was inferred from) SUPPORTS TRANSFER The curator's stated basis is the gene's own transport annotation on the same reference, which is itself an IMP. Not a gene-product donor, so no donor tracing applies. Supporting Evidence: PMID:9697856 Here, we show that mocha is a null allele of the delta subunit of the adaptor-like protein complex AP-3, which is associated with coated vesicles budding from the trans-Golgi network, and that AP-3 is missing in mocha tissues. PMID:9303295 Examination by light and electron microscopy indicated that these mutant flies have reduced numbers of eye pigment granules, which correlates with decreased levels of both pteridine (red) and ommachrome (brown) pigments. |
| GO:0032502 developmental process | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: A root-adjacent term carrying no information, from a rule whose published condition sets do not account for it. Reason: ARBA00028739 has 893 condition sets and AP3D1 satisfies none of them: no set names PTHR22781, and none of AP3D1's three FunFams (1.25.10.10:FF:000785, 1.25.10.10:FF:000808, 3.30.450.50:FF:000001) appears. I am not claiming the annotation is biologically false - HPS10 patients do have neurodevelopmental delay - only that the published rule cannot be shown to produce it, and that 'developmental process' is one step below the biological_process root and tells a reader nothing. The same provenance gap has been recorded for other ARBA rules in this repository. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00028739 Β· ARBA00028739 (GO:0032502 rule) SOURCE WEAK OR INFERRED 893 condition sets, none satisfiable by AP3D1's InterPro/Pfam/SMART/SUPFAM/PANTHER/FunFam complement as listed in the UniProt record and cross-checked against the InterPro API. The annotation cannot be reproduced from the rule as published. Supporting Evidence: PMID:26744459 AP3Ξ΄ deficiency thus causes a severe neurologic disorder with immunodeficiency and albinism that we propose to classify as HPS10. |
| GO:0035646 endosome to melanosome transport | IMP PMID:22511774 BLOC-2, AP-3, and AP-1 proteins function in concert with Rab... | KEEP AS NON CORE | Summary: Melanocyte instance of the AP-3 endosomal sorting step: tyrosinase and Tyrp1 reach maturing melanosomes from endosomal tubules via AP-3. Reason: The cached record for PMID:22511774 is abstract-only, so I am deferring to the curator on the experimental detail rather than second-guessing it; the annotation is in any case corroborated by direct AP-3-deficient melanocyte work showing tyrosinase mis-accumulation in endosomes. Kept as non-core for the same reason as melanosome organization: this is the melanocyte-specific readout of the generic endosome-to-lysosome sorting activity, which the core rows state directly. Supporting Evidence: PMID:22511774 These protein complexes control sorting and transport of newly synthesized integral membrane proteins from early endosomes to both lysosomes and LROs such as the melanosome. PMID:16162817 In AP-3-deficient melanocytes, tyrosinase accumulates inappropriately in vacuolar and multivesicular endosomes. |
| GO:0035651 AP-3 adaptor complex binding | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: A binding term applied to a constituent subunit of the very complex it names. AP3D1 is AP-3; GO:0030123 part_of already states the relation correctly. Reason: GO:0035651 is 'Binding to an AP-3 adaptor complex' - a function for proteins that engage AP-3 from outside it, such as BLOC-1 or PI4KIIalpha. The mouse source annotation is IDA from PMID:19010779, a crosslinking/mass-spectrometry study in which AP-3 complexes were purified and the associated proteins identified; the finding is that PI4KIIalpha and the BLOC complexes bind AP-3, not that delta binds AP-3 as an external partner. Applying the term to a subunit inverts the part/whole relation and duplicates, less accurately, what the three GO:0030123 part_of rows already say. Not removed, because delta does contact the other subunits, but it is an inverted and uninformative framing. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS SOURCE BUT NOT TARGET Mouse Ap3d1 carries GO:0035651 as IDA from PMID:19010779. The experiment is sound; the term assigns the binder role to a subunit of the complex being bound, and that misframing transfers with it. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS SOURCE BUT NOT TARGET Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:19010779 AP-3 was co-isolated with BLOC-1, BLOC-2, and homotypic fusion and vacuole protein sorting complex subunits; clathrin; and phosphatidylinositol-4-kinase type II alpha (PI4KIIalpha). PMID:26744459 AP3 complex formation and the degranulation defect in patient T cells were restored by retroviral reconstitution. |
| GO:0035654 clathrin-coated vesicle cargo loading, AP-3-mediated | NAS PMID:9545220 Association of the AP-3 adaptor complex with clathrin. | MODIFY | Summary: Cargo loading is right; the clathrin-coated-vesicle framing is not, and the clathrin contact that generated it was beta-3's, not delta's. Reason: Two independent problems with the same term. First, subunit attribution: the cited paper localises the clathrin interaction to the beta3 appendage domain, i.e. to AP3B1/AP3B2, proteins in a different PANTHER family (PTHR11134); nothing in it places clathrin on delta. Second, and decisively, the functional premise has since failed - acute chemical-genetic inactivation of clathrin leaves AP-3 endosomal budding intact, and the reconstituted human coat forms carriers from AP-3 arches and ARF1 dimers with no clathrin lattice at all. The GO definition of GO:0030123 already concedes that AP-3 does not associate with clathrin in all organisms. The cargo-loading claim survives intact, so the parent GO:0035459 vesicle cargo loading is proposed. Colocalisation of AP-3 with clathrin is not disputed (PMID:15051738, PMID:16162817) - the rejected claim is the functional one. Proposed replacements: vesicle cargo loading Supporting Evidence: PMID:9545220 In vitro binding assays showed that mammalian AP-3 did associate with clathrin by interaction of the appendage domain of its beta3 subunit with the amino-terminal domain of the clathrin heavy chain. PMID:23761069 These findings indicate that AP-3-clathrin association is dispensable for endosomal AP-3 vesicle budding and suggest that endosomal AP-3-clathrin interactions differ from those by which AP-1 and AP-2 adaptors productively engage clathrin in vesicle biogenesis. PMID:42139345 By demonstrating that AP3:ARF1 can generate carriers without using a clathrin lattice, we explain the clathrin independence of AP3-mediated trafficking. |
| GO:0036465 synaptic vesicle recycling | NAS PMID:15537701 Genetic analysis of the neuronal and ubiquitous AP-3 adaptor... | KEEP AS NON CORE | Summary: AP-3 regenerates synaptic vesicles from endosomes, which is part of the recycling cycle; a broad but defensible parent. Reason: Unlike the synaptic-vesicle-coating row from the same reference, this term does not commit to a mechanism AP-3 lacks. Rat neurons require AP-1 and AP-3 to regenerate vesicles from activity-dependent bulk endosomes, which is a recycling step, and the source paper's own result is about the membrane-protein content of synaptic vesicles. Kept as neuronal context. Supporting Evidence: PMID:22539861 A key event in this endocytosis mode is the generation of new vesicles from bulk endosomes, which replenish the reserve vesicle pool. PMID:15537701 Our results suggest that concerted nonredundant functions of neuronal and ubiquitous AP-3 provide a mechanism to control the levels of selected membrane proteins in synaptic vesicles. |
| GO:0043195 terminal bouton | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node, single mouse donor with a direct immuno-EM annotation. Correct, neuron-specific. Reason: PTN000513028 carries this on one gene-level donor, MGI:MGI:107734 (mouse Ap3d1, IDA from PMID:20089890), which put most AP-3 immunoreactivity in presynaptic axonal compartments. A single well-characterised donor is not weak evidence: the PAINT curator had the whole tree and alignment in view and placed the node at Bilateria, where synapses exist. Human is inside that clade and retains every mouse residue at the delta cargo-binding hinge. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The only gene-level donor on this row; IDA from PMID:20089890. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:0043195 terminal bouton | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Same mouse IDA by the automatic orthology route. Reason: Ensembl Compara transfer of the mouse Ap3d1 IDA from PMID:20089890; same verdict as the IBA row. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0043195 from PMID:20089890. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:0048490 anterograde synaptic vesicle transport | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node, mouse IMP donor: AP-3 is needed for cargo to leave the cell body for the synapse. Reason: Single gene-level donor MGI:MGI:107734, with its own IMP from PMID:21998198 showing that AP-3-BLOC-1 sorting acts in cell bodies upstream of nerve terminals. Correctly placed at Bilateria; correctly on delta, which is in both AP-3 forms. Neuron-specific context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The only gene-level donor on this row; IMP from PMID:21998198. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. Supporting Evidence: PMID:21998198 Reduction of PI4KIIΞ± in the dentate reflects a failure to traffic from the cell body. PMID:21998198 PI4KIIΞ± was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. |
| GO:0048490 anterograde synaptic vesicle transport | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Same mouse IMP by Ensembl Compara. Reason: Automatic orthology transfer of the mouse Ap3d1 IMP from PMID:21998198; same verdict as the IBA and ISS rows for this term. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IMP for GO:0048490 from PMID:21998198. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:21998198 PI4KIIΞ± was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. |
| GO:0048490 anterograde synaptic vesicle transport | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Curator sequence-similarity transfer of the same mouse IMP. Reason: One donor, mouse Ap3d1. The similarity judgement is easy to defend here: human and mouse delta are reciprocal 1:1 orthologs in PTHR22781:SF12 and align residue-for-residue over the ARF1 interfaces and the VAMP7-binding hinge, so no divergence argument stands against the transfer. Non-core for the tissue-context reason only. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The sole donor; mouse Ap3d1 IMP from PMID:21998198. Supporting Evidence: PMID:21998198 PI4KIIΞ± was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. |
| GO:0048499 synaptic vesicle membrane organization | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node, mouse IMP: AP-3 sets the membrane-protein composition of synaptic vesicles. Reason: Single gene-level donor MGI:MGI:107734, IMP from PMID:15860731 (Vglut1 and ZnT3 co-targeting to vesicles in PC12 cells). Corroborated by the beta3A/beta3B knockout comparison, in which synaptic-vesicle ZnT3 and ClC-3 content moves in opposite directions depending on which AP-3 form is missing - a result only interpretable if delta is in both. Neuronal context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The only gene-level donor on this row; IMP from PMID:15860731. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. Supporting Evidence: PMID:15537701 Surprisingly, despite the lack of neurological symptoms, beta3A-deficient mouse brain possessed significantly increased synaptic zinc stores and synaptic vesicle content of ZnT3 and ClC-3. PMID:17349999 Two forms of AP-3 have been characterized: a ubiquitous form, containing the Ξ΄, Ξ²3A, ΞΌ3A and Ο3(A/B) subunits, and a brain-specific form, containing Ξ²3B and ΞΌ3B in addition to the common Ξ΄ and Ο3(A/B) subunits |
| GO:0048840 otolith development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: From the mouse otoconia phenotype of the mocha allele. Inside the term's Vertebrata constraint, and matched by hearing loss in AP3D1 patients - but an organismal outcome, not a molecular role. Reason: Mouse Ap3d1 carries GO:0048840 as IMP from PMID:15109702, a gravity-receptor study in which mocha is one of the otoconia-deficient strains. GO:0048840 carries an only_in_taxon constraint to Vertebrata (taxId 7742, checked on the QuickGO constraints endpoint), so a human annotation violates nothing. The transfer is also independently plausible: inner-ear degeneration is part of the original mocha description, impaired hearing is part of the HPS10 phenotype, and a homozygous AP3D1 missense variant presents as sensorineural hearing loss. Non-core because this is several steps downstream of what delta does molecularly. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IMP for GO:0048840 from PMID:15109702; the mocha allele is one of five otoconia-deficient strains assayed. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:9697856 Here, we show that mocha is a null allele of the delta subunit of the adaptor-like protein complex AP-3, which is associated with coated vesicles budding from the trans-Golgi network, and that AP-3 is missing in mocha tissues. PMID:15109702 The purpose of the present study was to examine gravity receptor function in mutant mouse strains with variable deficits in otoconia: lethal milk (lm), pallid (pa), tilted (tlt), mocha (mh), and muted (mu). PMID:36445457 Loss-of-function variants in AP3D1 have been linked to Hermansky-Pudlak syndrome (HPS) 10, a severe multisystem disorder characterized by oculocutaneous albinism, immunodeficiency, neurodevelopmental delay, hearing loss (HL), and neurological abnormalities, fatal in early childhood. |
| GO:0060155 platelet dense granule organization | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: Platelet dense granules are lysosome-related organelles built by the AP-3 pathway; the storage-pool defect is documented in mocha mice and in HPS10 patients. Reason: The ComplexPortal NAS comes from a review, and that review states the HPS link rather than assaying AP-3 in platelets. The claim is nonetheless well supported by primary work not cited in the annotation: mocha is a platelet storage-pool deficiency model, and the second HPS10 family was shown to have an abnormal platelet storage pathway. Cell-type-specific outcome of the core sorting step. Supporting Evidence: PMID:23247405 For example, Hermansky-Pudlak Syndrome (HPS) patients and the corresponding animal models have abnormal melanosomes, platelet dense granules and lamellar bodies of lung type II epithelial cells. PMID:9697856 Here, we show that mocha is a null allele of the delta subunit of the adaptor-like protein complex AP-3, which is associated with coated vesicles budding from the trans-Golgi network, and that AP-3 is missing in mocha tissues. PMID:30472485 We further demonstrated an abnormal storage pathway in the platelets. |
| GO:0072657 protein localization to membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Broad but correct parent; the mouse donor arm has a real IMP behind it, while the ARBA arm cannot be reproduced. Reason: Two different kinds of support on one row. The Ensembl arm transfers mouse Ap3d1's IMP from PMID:16760431, where AP-3 deficiency mistargets LAMP1, PI4KIIalpha and VAMP7-TI - real evidence. The ARBA arm is weaker: ARBA00029167 has 26 condition sets, all FunFam-based, and none of AP3D1's three FunFams appears in any of them, so the rule as published does not account for the annotation. The term stands on the mouse arm. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00029167 Β· ARBA00029167 (GO:0072657 rule) SOURCE WEAK OR INFERRED 26 condition sets, all FunFam-based; none names any of AP3D1's three FunFams, so this arm cannot be reproduced from the published rule. UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IMP for GO:0072657 from PMID:16760431 -- this arm is what the annotation actually rests on. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:16760431 Mouse mutants that cause BLOC-1 or AP-3 deficiencies affected the targeting of LAMP1, phosphatidylinositol-4-kinase type II alpha, and VAMP7-TI. |
| GO:0072657 protein localization to membrane | IMP PMID:22511774 BLOC-2, AP-3, and AP-1 proteins function in concert with Rab... | KEEP AS NON CORE | Summary: Human experimental row from the melanocyte trafficking study; correct, and very general. Reason: The cached record is abstract-only, so I defer to the curator on the experimental detail. The claim itself - AP-3 controls where integral membrane proteins end up - is the generic description of the complex's job, and is stated more informatively by the endosome-to-lysosome and cargo-adaptor rows. Supporting Evidence: PMID:22511774 These protein complexes control sorting and transport of newly synthesized integral membrane proteins from early endosomes to both lysosomes and LROs such as the melanosome. |
| GO:0098793 presynapse | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mouse immuno-EM; presynaptic localisation of AP-3 in striatum and hippocampus. Reason: Mouse Ap3d1 carries GO:0098793 as IDA from PMID:20089890. Sound orthology transfer of a neuron-specific localisation. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0098793 from PMID:20089890. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:0098794 postsynapse | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Postsynaptic AP-3 acts in AMPA-receptor traffic to late endosomes/lysosomes during LTD. Reason: Mouse Ap3d1 carries GO:0098794 as IDA from PMID:20089890, and the postsynaptic role is independently established: stargazin binds AP-3A and that interaction routes AMPA receptors from early endosomes to late endosomes/lysosomes. A genuine second compartment for AP-3 in neurons, still neuron-specific context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0098794 from PMID:20089890; the postsynaptic function is separately documented in PMID:24217640. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:24217640 Here we show that stargazin, a transmembrane AMPA receptor regulatory protein, forms a ternary complex with adaptor proteins AP-2 and AP-3A in hippocampal neurons, depending on its phosphorylation state. |
| GO:0098830 presynaptic endosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node, mouse IDA: the early-endosomal compartment from which synaptic vesicles are regenerated. Reason: Single gene-level donor MGI:MGI:107734, IDA from PMID:19144828, which used high-resolution deconvolution microscopy to identify early endosomes where synaptic-vesicle and lysosomal membrane proteins coexist with AP-3 in neuronal cells. This is the neuronal version of the same endosomal compartment the Eukaryota node asserts generically, which is why the two nodes carry different terms for what is mechanistically one location. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The only gene-level donor on this row; IDA from PMID:19144828. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. Supporting Evidence: PMID:19144828 Using high-resolution deconvolution microscopy, we identified early endosomal compartments where both selected synaptic vesicle and lysosomal membrane proteins coexist with the adaptor protein complex 3 (AP-3) in neuronal cells. |
| GO:0098830 presynaptic endosome | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Same mouse IDA by Ensembl Compara. Reason: Automatic orthology transfer of the mouse Ap3d1 IDA from PMID:19144828; same verdict as the IBA row. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA for GO:0098830 from PMID:19144828. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:19144828 Using high-resolution deconvolution microscopy, we identified early endosomal compartments where both selected synaptic vesicle and lysosomal membrane proteins coexist with the adaptor protein complex 3 (AP-3) in neuronal cells. |
| GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Bilateria node; the mouse donor carries IDA, IEP and IMP for this term from the stargazin/AMPA-receptor LTD study. Reason: MGI:MGI:107734 is the single gene-level donor, and it is unusually well evidenced for this term - QuickGO shows IDA, IEP and IMP, all from PMID:24217640. That paper shows the stargazin-AP-3A interaction is required for AMPA receptors to reach late endosomes/lysosomes, and that blocking it upregulates surface recycling instead. Delta is a subunit of AP-3A, so the annotation is correctly placed. Neuron-specific context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:107734 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER The only gene-level donor; carries IDA, IEP and IMP for this term from PMID:24217640. PANTHER:PTN000513028 Β· PTHR22781 Bilateria (taxon:33213) IBD node PTN000513028 SUPPORTS TRANSFER Bilateria-level node; human AP3D1 is inside the inheriting clade. The node carries only the neuronal terms, while the complex and compartment terms sit on the deeper PTN000513025 -- the split is correct, because yeast has no synaptic vesicles. No IRD or IKR appears anywhere in the PTHR22781 PAINT slice. Supporting Evidence: PMID:24217640 Inhibiting the stargazin-AP-2 interaction disrupts NMDA-induced AMPA receptor endocytosis, and inhibiting that of stargazin-AP-3A abrogates the late endosomal/lysosomal trafficking of AMPA receptors, thereby upregulating receptor recycling to the cell surface. |
| GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Same mouse evidence by Ensembl Compara. Reason: Automatic orthology transfer of the mouse Ap3d1 IDA/IEP/IMP from PMID:24217640; same verdict as the IBA row. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA/IEP/IMP for GO:0098943 from PMID:24217640. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:24217640 Inhibiting the stargazin-AP-2 interaction disrupts NMDA-induced AMPA receptor endocytosis, and inhibiting that of stargazin-AP-3A abrogates the late endosomal/lysosomal trafficking of AMPA receptors, thereby upregulating receptor recycling to the cell surface. |
| GO:0098978 glutamatergic synapse | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: The synapse type in which the AP-3A/stargazin AMPA-receptor work was done. Reason: Mouse Ap3d1 carries GO:0098978 with IDA, IEP and IMP, all from PMID:24217640 - CA1 hippocampal glutamatergic synapses. A correct SynGO-style location annotation and a narrow one: it records where the experiment was done rather than a delta-specific property. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SUPPORTS TRANSFER Mouse Ap3d1 IDA/IEP/IMP for GO:0098978 from PMID:24217640. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SUPPORTS TRANSFER Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:24217640 Similarly, stargazin's interaction with AP-2 or AP-3A is necessary for low-frequency stimulus-evoked LTD in CA1 hippocampal neurons. |
| GO:0140916 zinc ion import into lysosome | IMP PMID:17349999 Zinc transporter 2 (SLC30A2) can suppress the vesicular zinc... | KEEP AS NON CORE | Summary: The delta-specific knockdown is sound, but AP-3 is not the zinc importer - it delivers the ZnT transporters that are. Reason: The experiment is squarely about this gene product: the siRNA targeted delta and depleted the complex, and vesicular zinc fell. The caveat worth recording is that AP-3 is not itself the zinc importer - GO:0140916 is 'The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a lysosome', a transmembrane transport event that ZnT2/ZnT3 perform - and the paper's own decisive result makes the point, since overexpressing GFP-ZnT2 RESCUES the AP-3-depleted phenotype, which is only interpretable if the AP-3 defect is a failure to deliver the transporter. I first proposed replacing the term with GO:0061462 protein localization to lysosome and have withdrawn that: GO:0061462 is an ancestor of GO:0006622 protein targeting to lysosome, which this review adds as a NEW row, so the substitution would have traded the zinc-specific content for a parent the file already carries, and no zinc-preserving alternative exists in GO for an upstream trafficking factor. For a biological process, involved_in also tolerates indirect-but-required participation in a way that a molecular-function term would not, and this is a curator IMP made from the full text. Kept, marked non-core: it is a downstream consequence of the generic AP-3 sorting step rather than delta's own activity. Supporting Evidence: PMID:17349999 For AP-3 protein complex knockdown, the target was the Ξ΄ subunit of the complex. PMID:17349999 Moreover, GFP-ZnT2 overexpression elicited a significant accumulation of zinc within mature lysosomes, which in untransfected M1 cells contained little or no chelatable zinc, and restored the zinc storage capability of AP-3-deficient cells. |
| GO:1903232 melanosome assembly | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: Complex-level statement that AP-3 is part of the machinery building melanosomes. Reason: Same review source and the same reasoning as the platelet dense granule row: correct, and strongly corroborated by primary work (garnet, mocha, HPS10 albinism, AP-3-deficient melanocytes). Cell-type-specific outcome rather than the core molecular role, and partly redundant with the melanosome organization IC. Supporting Evidence: PMID:23247405 Packaging of the tyrosinases into transport vesicles at early/recycling endosome-associated tubules is dependent on ubiquitous adaptor protein complex (AP)-1 and AP-3, and biogenesis of lysosome-related organelles complex (BLOC)-1 and BLOC-2. PMID:16162817 In AP-3-deficient melanocytes, tyrosinase accumulates inappropriately in vacuolar and multivesicular endosomes. |
| GO:1904115 axon cytoplasm | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: A GOC term-to-term inference from the two axonal-transport process annotations, not a localisation observation. Reason: The supporting entities on this row are GO terms, not gene products: GO:0008089 and GO:0048490, i.e. the inference is 'a protein involved in anterograde axonal transport is in axon cytoplasm'. That is sound as far as it goes, and the conclusion is corroborated by mouse immuno-EM placing AP-3 in presynaptic axonal compartments. But its content is entirely derived from the two process rows, both of which are themselves non-core neuronal context. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: GO:0008089 Β· GO:0008089 anterograde axonal transport (the process annotation this was inferred from) SUPPORTS TRANSFER A GO term, not a gene-product donor: the row is a term-to-term inference, so there is no donor record to trace. The underlying process row is itself an orthology transfer of a mouse IMP. GO:0048490 Β· GO:0048490 anterograde synaptic vesicle transport (the process annotation this was inferred from) SUPPORTS TRANSFER As above; the second process term feeding the same inference. Supporting Evidence: PMID:20089890 Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. |
| GO:1990742 microvesicle | IEA GO_REF:0000107 | REMOVE | Summary: GO:1990742 means an EXTRACELLULAR vesicle shed from the plasma membrane. The donor annotation uses 'microvesicle' in the source paper's sense of small INTRACELLULAR AP-3/BLOC-1 vesicles. Reason: The GO definition is explicit: 'An extracellular vesicle released from the plasma membrane and ranging in size from about 100 nm to 1000 nm.' The mouse donor annotation (IDA and IMP, PMID:16760431) is about a very different object - small vesicles isolated from cell homogenates that carry BLOC-1, AP-3 subunits and the AP-3 cargoes LAMP1, PI4KIIalpha and VAMP7-TI. A vesicle loaded with LAMP1 and a PI 4-kinase, recovered from a PC12 membrane fraction, is an intracellular transport intermediate, not a shed extracellular vesicle, and no AP-3 literature places delta on extracellular microvesicles. The defect is on the donor side and it propagates unchanged through Ensembl Compara. Mouse Ap3d1 has no review in this repository, so there is no upstream file to correct; the problem is recorded here instead. Propagation Review Root cause: SOURCE BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: UniProtKB:O54774 Β· mouse Ap3d1 (MGI:MGI:107734) SOURCE BAD Mouse Ap3d1 carries GO:1990742 as IDA and IMP from PMID:16760431. The experiment is real; the GO term chosen for it denotes an extracellular vesicle, while the paper's 'microvesicles' are intracellular AP-3/BLOC-1 transport intermediates. ensembl:ENSMUSP00000020420 Β· mouse Ap3d1 (Ensembl translation) SOURCE BAD Ensembl Compara protein id for the same mouse Ap3d1 record as UniProtKB:O54774 (Ensembl reports ENSMUSP00000020420 as a 1199-aa mouse translation, the length of O54774) -- one donor under two identifiers, not two independent sources. Supporting Evidence: PMID:16760431 we show that the BLOC-1 complex resides on microvesicles that also contain AP-3 subunits and membrane proteins that are known AP-3 cargoes PMID:16760431 Mouse mutants that cause BLOC-1 or AP-3 deficiencies affected the targeting of LAMP1, phosphatidylinositol-4-kinase type II alpha, and VAMP7-TI. |
| GO:0031267 small GTPase binding | IPI PMID:39705307 A structure-based mechanism for initiation of AP-3 coated ve... | NEW | Summary: Delta carries the primary ARF1-GTP binding site of AP-3 - two interfaces on the trunk, both required for membrane recruitment in cells. Reason: AP3D1 has no informative molecular function in GOA, yet its best-characterised subunit-level activity is binding the small GTPase ARF1. Reconstituted human AP-3 hemicomplexes show the binding is delta's, not beta-3's; the cryo-EM series resolves AP-3 engaging the membrane through the delta-ARF1 interface first; and in HeLa cells, mutating either of the two delta ARF1 interfaces (F77/M110/L111 and H157/K159/R163/R187) relocalises delta to the cytosol. All seven residues are present at those positions in O14617 (AP3D1-bioinformatics/delta_interfaces.tsv), and site 1 is conserved 3/3 across the PTHR22781 family from budding yeast to human while scoring 1/3 in every out-of-family adaptin large subunit. GO:0031267 is already used this way for the AP-1 large subunit AP1G1 and for AP3M1, both by IPI. Supporting Evidence: PMID:39705307 This suggests that the primary Arf1 binding site on AP-3 is on Ξ΄ PMID:39705307 it is apparent that the Ξ΄-Ο3 complex binds nearly as well as the full complex, with binding of the Ξ²3-ΞΌ3 hemicomplex barely above background levels in the Arf1GTP state PMID:42139345 These data indicate that Ξ΄ requires both ARF1 interfaces for correct membrane recruitment PMID:42139345 Mutations in AP3D1 that abolish interaction with ARF1 sites relocalize Ξ΄-WT-SG to the cytosol. |
| GO:0000149 SNARE binding | IPI PMID:22521722 Structural basis of the intracellular sorting of the SNARE V... | NEW | Summary: The delta hinge (residues 680-729) is a dedicated receptor for the longin domain of VAMP7, and only when VAMP7 is engaged in a cis-SNARE complex. Reason: A second missing molecular function, and one that is delta's alone rather than the complex's: the crystal structure (PDB 4AFI, whose chains A/B UniProt maps to O14617 680-729) resolves the delta linker bound to the VAMP7 longin domain, with a measured KD of 14 uM, and mutating I702/V704 or L709/L713 abolishes binding in vitro and in vivo while leaving complex assembly intact. In melanocytes the same interface is required for sorting: cells expressing VAMP7-non-binding delta fail to load a STX13-VAMP7 cis-SNARE complex into transport carriers and are hypopigmented. The four hinge residues are present in O14617 and are conserved 4/4 in mouse and bovine delta but 0/4 or 1/4 in AP3B1, AP1G1, AP2A1 and AP4E1, i.e. the interface is delta-private (AP3D1-bioinformatics/delta_interfaces.tsv). Supporting Evidence: PMID:22521722 We show that the linker of the Ξ΄-adaptin subunit of AP3 binds the VAMP7 longin domain and determines the structure of their complex. PMID:22521722 Mutation to serine of residues Ile702 and Val704 (mut1) and of Leu709 and Leu713 (mut2) in the Ξ΄-adaptin, which play key roles in the VAMP7:Ξ΄-adaptin interface PMID:22521722 The binding of VAMP7 to Ξ΄-adaptin requires the VAMP7 SNARE motif to be engaged in SNARE complex formation and hence AP3 must transport VAMP7 when VAMP7 is part of a cis-SNARE complex. PMID:33886957 Sorting requires either recognition of VAMP7 by the AP-3Ξ΄ subunit of AP-3 or of STX13 by the pallidin subunit of BLOC-1, but not both. |
| GO:0006622 protein targeting to lysosome | IMP PMID:42139345 Architecture of clathrin-independent AP3:ARF1-coated carrier... | NEW | Summary: The human-specific child of the IBA term: AP-3 delta delivers integral membrane cargo to lysosomes, and point mutants that break the coat break lysosomal cargo traffic in human cells. Reason: GOA carries the compartment-agnostic parent GO:0006623 protein targeting to vacuole by IBA from a yeast-seeded node, but not the lysosomal child that applies to human (GO:0006622 is_a GO:0006623, confirmed on the QuickGO ancestors endpoint). There is direct human loss-of-function evidence: HeLa cells in which endogenous delta was removed by transient CRISPR-KO and complemented with interface point mutants show disrupted lysosomal cargo trafficking. Independent support comes from AP-3-deficient cells mistargeting LAMP1 and from CLN3 requiring AP-3 for lysosomal delivery via its dileucine motif. The affinage deep-research record is cited on this row because its entire narrative is AP3D1 selecting cargo for lysosomal delivery (IFNGR1, DRAM2, RNF13). It is a lead, not evidence: no supporting_text is drawn from it, and each lead it offered was re-checked against its own PMID before being used. Supporting Evidence: PMID:42139345 Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. PMID:15598649 The dileucine motif of CLN3 bound both AP-1 and AP-3 in vitro, and expression of mutated CLN3 in AP-1- or AP-3-deficient mouse fibroblasts showed that both adaptor complexes are required for sequential sorting of CLN3 via this motif. PMID:15051738 Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes. |
| GO:0005198 structural molecule activity | IMP PMID:26744459 Mutations in AP3D1 associated with immunodeficiency and seiz... | NEW | Summary: Delta is a structural constituent of AP-3: without it the heterotetramer does not assemble, and restoring it restores the complex. Reason: AP3D1's only molecular-function rows in GOA are bare protein binding and an inverted AP-3-adaptor-complex-binding IEA, so the plainest subunit-level fact about the protein is unstated: delta holds the complex together. GO:0005198 is defined as 'The action of a molecule that contributes to the structural integrity of a complex', which is exactly the observation. The evidence is human and loss-and-restore: a homozygous AP3D1 mutation destabilises AP-3 in patient cells and retroviral re-expression of wild-type AP3D1 restores complex formation. The mouse mocha counterpart is the same result in reverse - the complex is destabilised in mocha fibroblasts and rescued by transfected delta, including by VAMP7-non-binding delta mutants, which shows the structural role is separable from the cargo-binding role. Added because core_functions asserts this activity and it should be traceable to an annotation. Supporting Evidence: PMID:26744459 Whole exome sequencing identified a homozygous mutation in AP3D1 that leads to destabilization of the adaptor protein 3 (AP3) complex. PMID:26744459 AP3 complex formation and the degranulation defect in patient T cells were restored by retroviral reconstitution. PMID:22521722 The absence of Ξ΄-adaptin causes destabilization of the AP3 complex in mouse mocha fibroblasts and mislocalization of VAMP7. PMID:22521722 Re-expression of wt and mutant Ξ΄-adaptin led to similar levels of stabilization of the other subunits of the complex |
| GO:0043316 cytotoxic T cell degranulation | IMP PMID:26744459 Mutations in AP3D1 associated with immunodeficiency and seiz... | NEW | Summary: HPS10 patient CD8+ T cells fail to degranulate, and retroviral re-expression of wild-type AP3D1 fully restores the response. Reason: Lytic granules are lysosome-related organelles, so this is the immune-cell instance of the AP-3 sorting pathway, and it is the phenotype that defined HPS10. The evidence is as clean as a human IMP gets: a homozygous AP3D1 mutation destabilises the complex, patient CD8+ T cell degranulation is reduced, and transduction with an AP3D1-containing vector - but not the empty vector - restores it to wild-type levels in two independent experiments. UniProt records the same conclusion in its FUNCTION block. Not currently in GOA for this gene. Supporting Evidence: PMID:26744459 AP3 complex formation and the degranulation defect in patient T cells were restored by retroviral reconstitution. PMID:26744459 Importantly, transduction with the AP3D1 containing vector fully restored the degranulation response of patient cells to levels of wild-type cells in two independent experiments |
| GO:0043320 natural killer cell degranulation | IMP PMID:26744459 Mutations in AP3D1 associated with immunodeficiency and seiz... | NEW | Summary: The degranulation defect in the HPS10 patient was most severe in fresh NK cells. Reason: Recorded separately from the T-cell term because the paper reports the NK phenotype separately and more severely, and because UniProt's FUNCTION block names both cell types. The evidence is the patient's own cells rather than the reconstitution experiment, which was done on T cells, so this row is the weaker of the two - but it is a direct loss-of-function observation in human NK cells and the cell biology (lytic granules are lysosome-related organelles built by AP-3) is the same. Supporting Evidence: PMID:26744459 It was most evident in fresh NK cells, where the response was very low and indistinguishable from that of patients with familial HLH, GS2 or CHS PMID:26744459 Since a number of immunodeficiencies with albinism are associated with impaired lymphocyte cytotoxicity, we analyzed expression of the degranulation marker CD107a on fresh |
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Download this section (compressed HTML)Q: Does the delta N-terminal amphipathic helix contribute membrane-bending activity to the AP3:ARF1 coat, or is its role limited to membrane association? The 2024 and 2026 structures reach opposite degrees of confidence on this.
Suggested experts: Baker RW, Briggs JAG, Owen DJ
Q: In mammalian cells, is there a productive trans-Golgi pool of AP-3, or is the tubular sorting endosome the only site where AP-3 makes carriers?
Suggested experts: Peden AA, Klumperman J, Bonifacino JS
Q: AP-3 is constitutively open, unlike AP-1 and AP-2, so what regulates when and where it engages cargo? Is the phosphorylated disordered linker of delta the switch?
Suggested experts: Ungermann C, Raunser S, Baker RW
Q: Beyond VAMP7, which cargoes does the delta hinge itself select, as opposed to the dileucine and YxxPhi cargoes captured by the sigma3/delta and mu3 sites?
Suggested experts: Owen DJ, Marks MS, Peden AA
Q: Which AP-3 cargo underlies the cochlear phenotype of HPS10 patients and the otoconial deficit of mocha mice - is Vangl2 sufficient to explain it?
Suggested experts: Faundez V, Chen P, Parzefall T
Experiment: Purify human AP-3 carrying wild-type delta, a helix-deleted delta, and a delta whose helix hydrophobic face is mutated to serine. Reconstitute with myristoylated ARF1-GTP on PI(3,5)P2-containing, cargo-bearing liposomes and score, by cryo-electron tomography, recruitment (AP-3 density per unit membrane) and tubulation (fraction of tubulated membrane, tube radius) as separate readouts. Wild-type delta and an ARF1-site-2 mutant are the positive and recruitment-null controls.
Hypothesis: The delta N-terminal amphipathic helix inserts into the outer leaflet and contributes to membrane deformation, so removing it will uncouple AP-3 recruitment from tubulation.
Type: in vitro reconstitution and cryo-electron tomography
Experiment: In HeLa cells with endogenous AP3D1 knocked out, re-express delta fused to an FKBP-rapamycin dimerisation module and acutely sequester it either at a TGN-anchored or at an endosome-anchored FRB. Follow a RUSH-released LAMP1-SBP-GFP reporter to lysosomes by live imaging. Rescue with untagged delta and with the ARF1 double-site mutant give the response range.
Hypothesis: The mammalian AP-3 budding step happens only on tubular sorting endosomes, so removing AP-3 selectively from the trans-Golgi will not delay lysosomal delivery of newly synthesised LAMP1.
Type: acute compartment-selective depletion with synchronised cargo release
Experiment: Map phosphosites by mass spectrometry on delta purified from cytosolic versus membrane-bound AP-3 fractions. Then complement AP3D1-knockout cells with phospho-null and phospho-mimetic delta and measure, separately, membrane recruitment (delta puncta per cell) and cargo capture (co-immunoprecipitation of VAMP7 and LAMP1, and lysosomal delivery of each).
Hypothesis: Phosphorylation of the delta linker (S758/S759 and neighbouring sites) gates cargo capture rather than membrane recruitment.
Type: phosphoproteomics with phospho-mutant complementation
Experiment: Use the delta hinge (residues 650-797) and the VAMP7-non-binding mut1/mut2 versions as baits in a proximity-labelling (TurboID) experiment in cells, and in parallel as GST baits against brain and melanocyte cytosol. Hits enriched on wild-type but not mut1/mut2 are candidate hinge cargoes; validate the top hits by testing whether their lysosomal delivery is rescued by wild-type but not by mut1/mut2 delta in AP3D1-knockout cells.
Hypothesis: The delta hinge selects additional SNARE or SNARE-complex cargoes beyond VAMP7, which would explain why delta-specific and complex-wide phenotypes differ.
Type: interface-mutant differential proximity labelling and pulldown
Experiment: Compare the surface and lysosomal proteomes of cochlear and vestibular epithelium from conditional Ap3d1-null and control mice at the onset of the phenotype, filtering for transmembrane proteins with cytosolic [DE]xxxL[LI] motifs. Test the top candidates plus Vangl2 for AP-3-dependent localisation, and for rescue of the polarity defect by motif-mutant versions that bypass AP-3.
Hypothesis: The hearing loss of AP3D1 deficiency is caused by mis-sorting of a specific dileucine-motif transmembrane cargo in the cochlea, with Vangl2 the leading candidate.
Type: tissue-restricted knockout proteomics with candidate validation
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: It is not established whether the amphipathic helix at the delta N-terminus actually deforms the membrane or merely binds it. Both structural papers stop at a proposal, and the 2026 coat paper attributes the helix array to mu3 'and possibly' delta.
OPEN BIOLOGY MF_DARK
What is known: What is established: AP-3 has low intrinsic membrane affinity and is recruited by ARF1-GTP through delta; the AP3:ARF1 coat does tubulate liposomes in vitro; and AlphaFold plus cryo-EM density support a helical N-terminal extension on delta in a position analogous to membrane-binding regions of other AP complexes.
Significance: It decides whether delta contributes an active membrane-bending activity (GO:0180020) or only a recruitment and cargo-capture function. Asserting the former from the current evidence would be an over-annotation, so the term is deliberately not proposed in this review.
What would resolve it: Helix-deleted and hydrophobic-face-mutant delta in a liposome tubulation assay with purified AP-3 and ARF1, read out by cryo-ET, separating tubulation from recruitment.
Provenance (the field's own admissions):
Gap: Whether mammalian AP-3 has a functional trans-Golgi pool that performs the Golgi-to-lysosome route its yeast ortholog performs, or whether the tubular sorting endosome is the only productive site, is unresolved.
NARROWING BIOLOGYCURATION BP_DARK
What is known: Established: yeast AP-3 buds alkaline phosphatase and Vam3p from the late Golgi; mammalian AP-3 is caught by immuno-EM budding from a tubular endosomal compartment and concentrates LAMP-1/LAMP-2 there; anti-delta immunofluorescence nevertheless shows a Golgi-region signal as well as peripheral structures.
Significance: It is the reason GO:0006896 Golgi to vacuole transport is propagated onto human AP3D1 from a yeast-seeded node. If a mammalian TGN pool is productive the IBA is fine as it stands; if not, the human annotation should be the endosomal route.
What would resolve it: Compartment-restricted acute depletion - e.g. TGN-anchored versus endosome-anchored ARF1-GAP recruitment, or a nanobody-based delta trap targeted to one compartment - with readout of newly synthesised LAMP1 arrival at lysosomes.
Provenance (the field's own admissions):
Gap: No function is assigned to the ~200-residue disordered, heavily phosphorylated region of delta C-terminal to the VAMP7-binding hinge (UniProt REGION 726-920, with phosphoserines at S758, S759 and elsewhere). It is not known what phosphorylates it or what the modification changes.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Established: the trunk (HEAT repeats 1-11, residues 34-585) carries the ARF1 and dileucine sites; the hinge at 680-729 binds VAMP7; the C-terminal appendage is the ear. The region between hinge and ear is disordered by MobiDB-lite and is the densest phosphosite cluster in the protein.
Significance: AP-1 and AP-2 are regulated by conformational switching that AP-3 does not use - AP-3 is constitutively open - so whatever tunes AP-3 activity must be something else, and a phosphorylated linker adjacent to the cargo-binding hinge is the obvious candidate.
What would resolve it: Phosphosite mapping on endosome-bound versus cytosolic AP-3, then phospho-null and phospho-mimetic delta in a VAMP7-sorting and LAMP1-delivery assay.
Provenance (the field's own admissions):
Gap: The cargo whose mis-sorting causes the hearing loss in AP3D1-deficient humans and the otoconial and inner-ear defects in mocha mice has not been identified.
NARROWING BIOLOGY BP_DARK
What is known: Established: mocha mice have inner-ear degeneration and graded otoconial deficits; HPS10 includes impaired hearing, and one family presents with sensorineural hearing loss as the leading manifestation; AP-3 is required for Vangl2 trafficking and inner-ear planar cell polarity in mouse.
Significance: Hearing loss is a presenting feature that can occur without the classic albinism-plus-bleeding picture, so it changes who gets tested for AP3D1 variants.
What would resolve it: Cochlear and vestibular proteomics of conditional Ap3d1-null inner ear, prioritising dileucine-motif transmembrane proteins, with Vangl2 as the current lead.
Provenance (the field's own admissions):
Gap: Why BLOC-1 controls AP-3-dependent synaptic-vesicle biogenesis in the dentate gyrus but not in the striatum is unknown, even though both complexes are ubiquitously expressed.
OPEN BIOLOGY BP_DARK
What is known: Established: AP-3 and BLOC-1 physically associate, share vesicles and cargo, and form a super-complex that sorts a cis-SNARE complex; loss of AP-3 decreases synaptic-vesicle size in striatum but increases it in dentate gyrus; BLOC-1 loss reduces presynaptic AP-3 in dentate gyrus only.
Significance: It is the clearest evidence that AP-3 output is regulated by something other than its own subunit composition, and it bears on the dysbindin/BLOC-1 link to schizophrenia.
What would resolve it: Region-resolved comparison of the AP-3 interactome and cargo repertoire between striatum and dentate gyrus in wild-type and BLOC-1-null mice.
Provenance (the field's own admissions):
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