AP1S3 encodes sigma-1C (also called sigma-3), one of three interchangeable small subunits of adaptor protein complex 1 (AP-1), the heterotetrameric clathrin adaptor that selects cargo for transport between the trans-Golgi network and endosomes. AP-1 comprises two large adaptins (gamma and beta-1), a medium adaptin (mu-1A or mu-1B) and a single small adaptin, which in human cells may be sigma-1A, sigma-1B or sigma-1C, so the sigma-1C form is a variant of the same complex rather than a distinct machine. The tetramer is cytosolic at rest and is recruited onto trans-Golgi and endosomal membranes by ARF1 and phosphoinositides, where it forms the inner layer of a clathrin coat, captures transmembrane cargo, rides the budded vesicle to its destination and is released again on uncoating. Within the complex the sigma subunit is the chain that reads acidic dileucine sorting signals, [DE]XXXL[LI], in the cytosolic tails of cargo proteins. Structures containing sigma-1C itself show the two bulky motif residues inserted into adjacent hydrophobic pockets formed by Leu65, Phe67, His85, Val88 and Val98, with Lys60 and Arg61 forming a basic patch that hydrogen-bonds a phosphoserine immediately downstream of the motif, so that phosphorylation of a cargo tail can strengthen its capture. The same surface is occupied, before the tetramer is assembled, by the pseudoGTPase domain of the assembly chaperone AAGAB, which keeps the free sigma subunit folded and soluble and sterically blocks cargo binding until the complex is built. Sigma-1C is a 154-residue longin/roadblock-fold protein with no catalytic activity, and it also contributes to the structural integrity of the tetramer through an interface with the medium adaptin. Loss of sigma-1C is tolerated at the organismal level, consistent with the three sigma-1 paralogues being largely redundant, but it has clear cellular consequences. Cells depleted of it fail to deliver Toll-like receptor 3 to endosomes and lose the type I interferon response to double-stranded RNA, and they form fewer autophagosomes on starvation. In the epidermis, where the gene is abundantly expressed, these defects converge on an inflammatory circuit in which the autophagy receptor p62 accumulates, NF-kappa-B is activated and interleukin-36-alpha is overproduced. Two hypomorphic coding variants - Phe4Cys, which destabilises the protein's hydrophobic core, and Arg33Trp, which weakens the interface with the medium adaptin - are enriched in people with pustular psoriasis; neither lies on the cargo-binding surface, so both act by reducing the amount of functional complex rather than by changing what it selects.
Definition: Binding to an acidic dileucine sorting signal, a [DE]XXXL[LI] peptide motif in the cytosolic tail of a transmembrane cargo protein, which directs that protein into clathrin-coated vesicles formed by heterotetrameric adaptor protein complexes.
Justification: GO can express the complex-level activity (GO:0035615 clathrin-cargo adaptor activity) and the tyrosine-motif counterpart read by the medium adaptin (GO:0089710 endocytic targeting sequence binding, whose definition requires an essential tyrosine), but it has no term for the dileucine motif read by the small adaptin. That leaves the one activity a sigma subunit demonstrably performs on its own unexpressible, so sigma subunits across AP-1, AP-2 and AP-4 carry either nothing or a bare protein binding row. The gap is now sharply defined by structure: the motif's two bulky residues occupy adjacent pockets on the sigma subunit, and in AP1S3 those pockets are formed by Leu65, Phe67, His85, Val88 and Val98. A sibling of GO:0089710 under protein binding would fit the existing pattern exactly. The absence was checked by searching the GO release served by QuickGO on 'dileucine', 'sorting signal binding', 'cargo adaptor activity', 'signal sequence binding' and 'endosomal sorting signal'; 'dileucine' returns nothing at all.
Parent term: protein binding
Supporting Evidence:
Definition: Binding to an assembly chaperone, a protein that binds an individual subunit or an assembly intermediate of a multi-subunit complex and is required for that complex to form correctly, but that is not itself a component of the finished complex.
Justification: Dedicated assembly chaperones are recognised for ribosomes, proteasomes, nucleosomes and SNARE complexes as well as for the AP-1 and AP-2 adaptors, but GO has no term for the client side of that relationship: searching the ontology on 'assembly chaperone', 'chaperone binding' and 'protein complex assembly' returns only GO:0051087 protein-folding chaperone binding, whose definition is about nascent or unfolded polypeptides. For AP1S3 the relationship is unusually well defined - a 1.68 A co-crystal with the AAGAB pseudoGTPase domain, a 994 A2 interface, a 1:1 complex, and the demonstration that the free subunit is otherwise misfolded - yet GO does not even classify AAGAB itself as a chaperone, so the client-side annotation currently has to borrow a folding-chaperone term. A term of this shape would serve every AP-complex sigma and alpha/gamma subunit, not just this one.
Parent term: protein binding
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-421831 | ACCEPT | Summary: Reactome's trans-Golgi Network Coat Assembly reaction places AP-1, with AP1S3 in the sigma slot, on the Golgi membrane as the clathrin coat is nucleated. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face file:human/AP1S3/AP1S3-uniprot.txt PDB; 7R4H; EM; 2.34 A; S=1-154. |
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-421833 | ACCEPT | Summary: Reactome places AP-1 on the Golgi membrane while it binds VAMP cargo and captures it into the forming coat. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Cargo capture is precisely the step in which the sigma subunit's sorting-signal pocket is engaged. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face PMID:36261523 STING L364 and I365 of the EXXXLI sorting motif engage L65, F67, H85, V88 and V98 of the σ subunit through hydrophobic interactions |
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-421835 | ACCEPT | Summary: Reactome's trans-Golgi Network Vesicle Scission reaction has the AP-1 coat, including AP1S3, still on the Golgi membrane as the vesicle is released. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face |
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-432706 | ACCEPT | Summary: Reactome places AP-1 on the Golgi membrane during coat assembly on the lysosome-destined TGN vesicle. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; PMID:36261523 The most prominent adaptor protein complex that is involved in cargo shuttling from the TGN to endolysosomes is AP-1 |
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-432707 | ACCEPT | Summary: Reactome's trans-Golgi Network Lysosomal Vesicle Scission reaction has the AP-1 coat on the Golgi membrane at the moment of scission. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face |
| GO:0000139 Golgi membrane | TAS Reactome:R-HSA-432712 | ACCEPT | Summary: Reactome places AP-1 on the lysosome-vesicle-destined Golgi membrane while it binds VAMP and captures cargo. Reason: AP-1 is recruited from the cytosol onto Golgi/TGN membranes, where it forms the inner layer of the clathrin coat; UniProt records this entry as a Golgi apparatus protein and as part of the coat on the cytoplasmic face of Golgi-derived vesicles. Reactome models the AP-1 sigma slot as a set, so AP1S3 inherits this reaction rather than being tested in it, but the location is correct for the sigma-1C form: AP1S3 is chain S of the ARF1-activated, membrane-recruited AP-1 core in PDB 7R4H. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; PMID:36261523 The most prominent adaptor protein complex that is involved in cargo shuttling from the TGN to endolysosomes is AP-1 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MODIFY | Summary: A proteome-scale yeast two-hybrid screen reported AP1S3 binding AAGAB (Q6PD74). The partner is now known at 1.68 A: AAGAB is the assembly chaperone for AP-1 and AP-2, and its pseudoGTPase domain caps AP1S3's cargo pocket. Reason: Bare protein binding says nothing about what AP1S3 does. The partner resolves to AAGAB, the only curated binary interactor in this entry's UniProt INTERACTION block, and the interaction now has structural and functional follow-up: a 1.68 A co-crystal of AAGAB's pseudoGTPase domain with full-length AP1S3 (PDB 9DDT), a 994 A2 interface, pull-downs showing the pseudoGTPase domain is necessary and sufficient, and the demonstration that AAGAB is what allows a sigma subunit to fold and stay soluble at all. GO offers no 'assembly chaperone binding' term - searching the ontology on 'assembly chaperone', 'chaperone binding' and 'protein complex assembly' returns GO:0051087 protein-folding chaperone binding as the only chaperone-binding molecular function - and AAGAB demonstrably performs a folding function on this client, so GO:0051087 is the informative replacement. One caveat is recorded rather than hidden: GO does not itself classify AAGAB as a chaperone - its own record (Q6PD74) carries protein binding as its only molecular function - so the replacement rests on what PMID:40752490 demonstrates about the partner, not on an existing GO classification of it. The cleaner fix would be a dedicated assembly-chaperone-binding term, which is filed under proposed_new_terms. Proposed replacements: protein-folding chaperone binding Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt Q96PC3; Q6PD74: AAGAB; NbExp=6; IntAct=EBI-3923129, EBI-719906; PMID:40752490 AAGAB is the assembly chaperone for AP1 and AP2 adaptor complexes that are key to clathrin-mediated membrane trafficking. PMID:40752490 we determined the crystal structure of wild type AAGAB psGD in complex with AP1σ3 at the resolution of 1.68 Å PMID:40752490 To confirm that AAGAB aids the solubility and folding of σ subunits PMID:40752490 Yet this small amount of σ subunit was mostly misfolded PMID:25416956 high-quality human binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MODIFY | Summary: BioPlex affinity-purification mass spectrometry independently recovered the same AAGAB (Q6PD74) interaction, this time from cells rather than from two-hybrid. Reason: Same judgement as the two-hybrid row, and the orthogonal method matters: a Y2H hit and an AP-MS hit for the same partner, plus a co-crystal, is a well-supported interaction rather than a screen artefact. The replacement term is chosen for the same reason - AAGAB is the AP-1/AP-2 assembly chaperone and is required for sigma-subunit folding and solubility, and it forms a 1:1 complex with AP1S3 - so protein-folding chaperone binding captures what the interaction is for, whereas protein binding does not. Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:33961781 Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. PMID:40752490 GST-AP1σ3 was able to pull down FL AAGAB and psGD, but not AAGABΔpsGD PMID:40752490 The psGD:AP1σ3 interface buries an area of 994 Å2 PMID:40752490 Both the elution position and the SDS-PAGE of SEC peak fractions suggest a 1:1 stoichiometry between AAGAB psGD and AP1σ3 file:human/AP1S3/AP1S3-uniprot.txt PDB; 9DDT; X-ray; 1.68 A; B=1-154. |
| GO:0005765 lysosomal membrane | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: ComplexPortal assigns lysosomal membrane to the sigma1C AP-1 variant (CPX-5049) on the strength of a review of lysosome-related organelle biogenesis. Reason: AP-1 reaches the lysosomal membrane only as the coat of a delivering vesicle, at the docking and uncoating step; it is not a compartment where AP-1 resides. UniProt's SUBCELLULAR LOCATION for this entry lists Golgi apparatus, cytoplasmic vesicle membrane and clathrin-coated pit, and does not list the lysosome. The cited source is a review of Rab32/Rab38-directed traffic that makes an AP-1-complex-level statement with no sigma-1C experiment in it. Defensible as a transient, pathway-terminal location; not a core AP1S3 localisation. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. PMID:23247405 redirect the ubiquitous machinery-BLOC-2, AP-1 and AP-3-to traffic specialized cargoes to melanosomes in melanocytes |
| GO:0005765 lysosomal membrane | TAS Reactome:R-HSA-432688 | KEEP AS NON CORE | Summary: Reactome's trans-Golgi Network Derived Lysosomal Vesicle Uncoating reaction places the AP-1 coat at the lysosomal membrane at the moment it is shed. Reason: The same reasoning as the ComplexPortal row: this is the coat on a vesicle that has just docked, captured at the instant before disassembly. It is a real step in the pathway AP-1 serves, so the row is not wrong, but a steady-state lysosomal-membrane localisation is not supported for AP1S3 and UniProt does not assert one. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; PMID:36261523 The most prominent adaptor protein complex that is involved in cargo shuttling from the TGN to endolysosomes is AP-1 |
| GO:0005765 lysosomal membrane | TAS Reactome:R-HSA-432707 | KEEP AS NON CORE | Summary: Reactome also places the coat at the lysosomal membrane in the lysosomal vesicle scission reaction. Reason: Peripheral for the same reason as the other two lysosomal-membrane rows: AP-1 is present on the membrane of the vesicle in transit to the lysosome rather than on the lysosome as a resident compartment. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; |
| GO:0005769 early endosome | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | ACCEPT | Summary: ComplexPortal assigns early endosome to the sigma1C AP-1 variant. The endosome is one of the two compartments AP-1 works between. Reason: This is core AP-1 cell biology and is stated independently in the primary literature on this gene: AP-1 shuttles cargo between the trans-Golgi network and the endosomes, and the AP1S3 disease paper opens with exactly that statement. The endosomal arm is also where the one AP1S3-specific loss-of-function phenotype lives - TLR3 fails to reach the endosome when AP1S3 is silenced. Supporting Evidence: PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. PMID:24791904 We found that TLR-3 trafficking was disrupted in both knockdown cell lines, where the ratio between endosomal and newly synthesized receptor was markedly reduced. file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000044 | ACCEPT | Summary: Automatic mapping of this entry's own UniProt Golgi apparatus subcellular-location term. Reason: Not a homology transfer: GO_REF:0000044 translates a location UniProt curators asserted on this very entry, and that assertion rests on the AP-1 complex's well-established Golgi/TGN recruitment. Consistent with the Reactome TAS rows and with AP1S3 being the sigma chain of the membrane-recruited AP-1 core in PDB 7R4H. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0132 · UniProtKB Subcellular Location SL-0132 (Golgi apparatus) SUPPORTS TRANSFER The SubCell term is asserted on this entry's own SUBCELLULAR LOCATION line, which names the Golgi apparatus and describes the protein as part of the coat on Golgi-derived vesicles; the GO_REF:0000044 mapping is a one-to-one vocabulary translation, not a homology transfer. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face file:human/AP1S3/AP1S3-uniprot.txt PDB; 7R4H; EM; 2.34 A; S=1-154. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-182263 | ACCEPT | Summary: Reactome's Degradation of MHC I Complex reaction, part of the HIV-1 Nef pathway, has AP-1 present as a cytosolic complex. Reason: AP complexes are cytosolic heterotetramers that cycle on and off membranes, so a cytosol localisation for the unrecruited pool is correct, independent of the reaction context. The Nef pathway is a viral hijack of AP-1, which makes the process peripheral, but this row is a location claim and the location is right. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-182279 | ACCEPT | Summary: Reactome has cytosolic AP-1 forming the MHC I:Nef:AP-1:PACS-1 complex. Reason: Same judgement: the cytosolic pool of AP-1 is the form recruited into such complexes, and AP complexes are explicitly described as cytosolic heterotetramers in this gene's own primary literature. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-182286 | ACCEPT | Summary: Reactome's transport step for the MHC I:Nef:AP-1:PACS-1 complex again lists AP-1 in the cytosol. Reason: A correct location claim for the soluble AP-1 tetramer; the Nef context does not change where the complex is. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-2130619 | ACCEPT | Summary: Reactome's TGN-lysosomal vesicle coat assembly reaction draws AP-1 from the cytosol onto the membrane. Reason: Coat assembly begins with a cytosolic adaptor, so cytosol is the correct compartment for the input form of AP-1 in this reaction. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. PMID:24791904 Each of the five known complexes (AP-1, AP-2, AP-3, AP-4, and AP-5) is active in a distinct subcellular compartment, where it mediates the delivery of transmembrane proteins to specific target organelles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-2213236 | ACCEPT | Summary: Reactome returns AP-1 to the cytosol when the TGN-lysosome vesicle uncoats. Reason: Uncoating releases the adaptor back into the cytosol, which is where the tetramer resides between rounds of recruitment. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-421833 | ACCEPT | Summary: Cytosolic AP-1 in Reactome's VAMP-binding and cargo-capture reaction at the TGN. Reason: Correct for the soluble pool of the complex; the same reaction also generates the Golgi membrane row reviewed above, which is the membrane-bound end of the same cycle. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-421836 | ACCEPT | Summary: Reactome's trans-Golgi Network Derived Vesicle Uncoating reaction returns AP-1 to the cytosol. Reason: The adaptor is released into the cytosol on uncoating; this is the resting compartment of the tetramer. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-432688 | ACCEPT | Summary: Cytosolic AP-1 released by uncoating of the TGN-derived lysosomal vesicle. Reason: Same cycle, same correct compartment for the released adaptor. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-432712 | ACCEPT | Summary: Cytosolic AP-1 in Reactome's cargo-capture reaction on the lysosome-vesicle-destined Golgi membrane. Reason: Correct for the soluble form of the complex entering the reaction. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8951498 | ACCEPT | Summary: Reactome's dissociation of the Arf1:GDP, AP-1 clathrin-coated nonameric complex leaves AP-1 in the cytosol. Reason: ARF1 GTP hydrolysis releases AP-1 from the membrane back into the cytosol. The ARF1-activated state is exactly the one captured in PDB 7R4H, in which AP1S3 is the sigma chain, so both ends of this cycle are structurally documented for this protein. Supporting Evidence: PMID:24791904 Adaptor protein (AP) complexes are cytosolic heterotetramers that promote the assembly and trafficking of small transport vesicles. file:human/AP1S3/AP1S3-uniprot.txt PDB; 7R4H; EM; 2.34 A; S=1-154. |
| GO:0005905 clathrin-coated pit | IEA GO_REF:0000044 | ACCEPT | Summary: Automatic mapping of this entry's own UniProt clathrin-coated pit location. Reason: The GO definition of clathrin-coated pit explicitly includes pits that form in the trans-Golgi network and on endosomes, not only at the plasma membrane, so it is the right term for an AP-1 subunit. UniProt asserts the location and the Coated pit keyword on this entry directly. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0069 · UniProtKB Subcellular Location SL-0069 (Coated pit) SUPPORTS TRANSFER Asserted on this entry ('Membrane, clathrin-coated pit' in SUBCELLULAR LOCATION, and the Coated pit keyword). AP-1 nucleates clathrin-coated buds on the TGN, which the GO term's definition explicitly covers alongside plasma-membrane pits. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt 3D-structure; Alternative splicing; Coated pit; Cytoplasmic vesicle; PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0006605 protein targeting | IMP PMID:24791904 AP1S3 mutations are associated with pustular psoriasis and i... | MODIFY | Summary: Silencing AP1S3 disrupted delivery of TLR3 to the endosome in two stable shRNA-knockdown HaCaT keratinocyte lines and, independently, in an AP1S3-knockdown HEK293 line; in the HaCaT lines TLR3-driven IFNB1 induction was additionally abolished. The GO term chosen for it, protein targeting, is the generic parent and loses what was measured. Reason: The experiment is sound and the evidence code is right: this is stable shRNA knockdown, i.e. IMP, not IDA. What it measured was specifically where TLR3 ends up - the ratio of endosomally processed to newly synthesised receptor - so protein localization to endosome (GO:0036010) states the finding, while protein targeting states only that some protein goes somewhere. UniProt independently summarises this paper as 'Involved in TLR3 trafficking'. Keeping the parent would discard the one compartment-resolved loss-of-function result this gene has. Which readout came from which background matters and is kept separate here: the two stable shRNA lines were made in HaCaT keratinocytes and carry both the TLR3-processing and the IFNB1 results, while a third, separately generated AP1S3-knockdown line in HEK293 reproduced the TLR3-processing defect only. The localisation defect is therefore not keratinocyte-specific, but the interferon readout was measured only in keratinocytes. Proposed replacements: protein localization to endosome Supporting Evidence: PMID:24791904 We found that TLR-3 trafficking was disrupted in both knockdown cell lines, where the ratio between endosomal and newly synthesized receptor was markedly reduced. PMID:24791904 the induction of IFNB1 transcripts was virtually abolished in one knockdown cell line and significantly reduced in the second PMID:24791904 we generated two stable AP1S3 -knockdown cell lines ( Figure 3 A) through the lentiviral transduction of HaCaT immortalized keratinocytes with targeted small hairpin RNA (shRNA) constructs PMID:24791904 We generated another AP1S3 -knockdown cell line by silencing gene expression in HEK293 cells PMID:24791904 In keeping with the results obtained in HaCaT keratinocytes, we were able to show that AP1S3 deficiency resulted in reduced processing of transfected TLR-3 PMID:24791904 We stimulated control and knockdown cell lines with poly(I:C) and measured IFNB1 expression by real-time PCR. file:human/AP1S3/AP1S3-uniprot.txt Involved in TLR3 trafficking (PubMed:24791904). file:human/AP1S3/AP1S3-deep-research-affinage.md AP1S3 is required for endosomal translocation of TLR3, and its depletion mislocalizes TLR3 and blunts downstream TLR3 signaling |
| GO:0006886 intracellular protein transport | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the pan-AP-complex small-chain conserved site to intracellular protein transport. Reason: Correct and appropriately generic. IPR000804 is the clathrin adaptor small-chain PROSITE site shared by AP-1 to AP-4 sigma subunits, which act in different compartments, so the parent term is the honest level for a signature that cannot tell them apart. The claim itself is not in doubt for AP1S3. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR000804 · InterPro IPR000804, Clathrin adaptor complex small chain conserved site (PROSITE PS00989) SUPPORTS TRANSFER AP1S3 matches this signature (UniProt lists PROSITE PS00989 CLAT_ADAPTOR_S). It is a pan-AP-complex small-chain site, so the terms mapped from it are correspondingly general, but they are not wrong for any member. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt Belongs to the adaptor complexes small subunit family. PMID:24791904 Each of the five known complexes (AP-1, AP-2, AP-3, AP-4, and AP-5) is active in a distinct subcellular compartment, where it mediates the delivery of transmembrane proteins to specific target organelles. |
| GO:0015031 protein transport | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the AP complex small subunit family signature to protein transport. Reason: Broader still than the row above - protein transport is the parent of intracellular protein transport - but not wrong, and the GOA record legitimately carries both a general and a more specific version of the same claim from two different signatures. IPR016635 is the family-wide PIRSF for AP complex small subunits, so the generic term matches the signature's resolution. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR016635 · InterPro IPR016635, AP complex small subunit (PIRSF015588) SUPPORTS TRANSFER AP1S3 matches PIRSF015588. The signature is family-wide across AP-1 to AP-4 small subunits, so the mapped term is the generic protein-transport parent. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt Belongs to the adaptor complexes small subunit family. |
| GO:0016192 vesicle-mediated transport | IBA GO_REF:0000033 | ACCEPT | Summary: The one phylogenetic annotation on this gene: vesicle-mediated transport, inherited from the PTHR11753 ancestral node PTN000204281, which was seeded by AP-1, AP-2 and AP-3 sigma subunits across fungi, worm, fly, rodent and human. Reason: The node placement is sound and AP1S3 is inside the clade that inherited the function. Ten of the eleven gene-level donors carry experimental evidence, but they carry it in different descendant branches - Golgi-to-vacuole transport in the two yeast AP-3/AP-1 sigmas and Candida APS3, endosome-to-Golgi transport in mouse Ap1s1 and pombe aps1, clathrin-dependent endocytosis in worm aps-2 and human AP2S1, synaptic-vesicle and postsynaptic-receptor internalisation in mouse Ap1s2 and rat Ap2s1. That divergence is exactly why the parent vesicle-mediated transport is the correct least common ancestor here: any more specific child would name one compartment and be wrong for the rest of the clade, so this is not a granularity failure. AP1S3 retains the whole sigma fold and, as the structures show, a functional cargo-binding surface, and nothing in the family slice records a loss (no IRD or IKR row exists for PTHR11753). AP1S3 is not among its own donors, so this is not a self-referential IBA - it is a genuine outward transfer to a gene with no experimental annotation of its own for the term. Propagation Review Root cause: NO FAILURE CORE Sources checked: CGD:CAL0000182525 · APS3, Candida albicans AP-3 sigma (Q59QC5) SUPPORTS TRANSFER Carries GO:0006896 Golgi to vacuole transport by IMP (PMID:20870878), a descendant of the propagated term. FB:FBgn0039132 · AP-1sigma (CG5864), Drosophila melanogaster SOURCE WEAK OR INFERRED The only donor without experimental evidence under GO:0016192: its QuickGO record carries IEA and ISS codes only, and all its UniProt entries are TrEMBL. It adds phylogenetic breadth but no independent experimental support. FB:FBgn0043012 · AP-2sigma (CG6056), Drosophila melanogaster (Q9VDC3) SUPPORTS TRANSFER Carries GO:0035615 clathrin-cargo adaptor activity by IMP (PMID:20226669) and GO:0016192 by NAS. Present in the 2025 IBA WITH/FROM but seeded on this node's other IBD row (GO:0043231) in the 2026 PAINT refresh - a snapshot-date difference, not a defect. MGI:MGI:1098244 · Ap1s1 (sigma-1A), mouse (P61967) SUPPORTS TRANSFER The mouse orthologue of AP1S3's closest paralogue; carries GO:0042147 retrograde endosome-to-Golgi transport by IMP (PMID:24928897). MGI:MGI:1889383 · Ap1s2 (sigma-1B), mouse (Q9DB50) SUPPORTS TRANSFER Carries GO:0016192 itself by IMP (PMID:24928897), plus synaptic-vesicle recycling and endocytosis terms by IDA/IMP (PMID:20203623). PANTHER:PTN000204281 · PTHR11753 (adaptor complexes small subunit family) IBD node for GO:0016192 SUPPORTS TRANSFER The family PAINT slice contains exactly two IBD rows, both on this node: GO:0016192 (P) and GO:0043231 (C). Its seeds span AP-1, AP-2 and AP-3 sigma subunits from fungi, worm, fly, rodent and human, so the node is at least as deep as the eukaryotic divergence of the AP complexes, and AP1S3 is inside it - PANTHER classifies AP1S3 into PTHR11753 with no subfamily assignment. No IRD or IKR row appears anywhere in this family's slice, and the slice format does carry those codes for other families, so their absence is informative rather than an artefact of the extract. PomBase:SPAP27G11.06c · aps1/vas2, Schizosaccharomyces pombe AP-1 sigma (Q9P7N2) SUPPORTS TRANSFER Carries GO:0042147 and GO:0099638 by IDA (PMID:19624755). RGD:620188 · Ap2s1, rat AP-2 sigma (P62744) SUPPORTS TRANSFER Carries GO:0098884 postsynaptic neurotransmitter receptor internalization by EXP, IDA and IMP (PMID:17289840). SGD:S000003561 · APS3, Saccharomyces cerevisiae AP-3 sigma (P47064) SUPPORTS TRANSFER Carries GO:0006896 Golgi to vacuole transport by IMP (PMID:9335339). SGD:S000004160 · APS1, Saccharomyces cerevisiae AP-1 sigma (P35181) SUPPORTS TRANSFER Carries GO:0006896 Golgi to vacuole transport by IMP (PMID:17003107). UniProtKB:P53680 · AP2S1, human AP-2 sigma SUPPORTS TRANSFER Carries GO:0048488 synaptic vesicle endocytosis by IDA and IMP (PMID:11102472) and GO:0072583 clathrin-dependent endocytosis by TAS. It is a paralogue, not the target, and it is in the family index as a PTHR11753 member. WB:WBGene00000157 · aps-2, Caenorhabditis elegans AP-2 sigma (Q19123) SUPPORTS TRANSFER Carries GO:0072583 clathrin-dependent endocytosis by IMP (PMID:25303366). Resolved via a UniProt free-text lookup; the wormbase xref query returns no hit for this gene id. Supporting Evidence: PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. file:human/AP1S3/AP1S3-uniprot.txt Belongs to the adaptor complexes small subunit family. PMID:36261523 STING L364 and I365 of the EXXXLI sorting motif engage L65, F67, H85, V88 and V98 of the σ subunit through hydrophobic interactions file:human/AP1S3/AP1S3-bioinformatics/RESULTS.md The cargo-facing surface of AP1S3 is intact and structurally characterised at 1.68-2.34 A |
| GO:0016192 vesicle-mediated transport | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping to vesicle-mediated transport from two signatures, one pan-AP and one AP-1-sigma specific. Reason: Agrees with the IBA at the same grain and from an independent line of evidence. One of the two signatures, IPR044733 (CDD cd14831 AP1_sigma), is AP-1-sigma specific rather than pan-family, so this row is not merely a restatement of the generic small-chain site. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR000804 · InterPro IPR000804, Clathrin adaptor complex small chain conserved site (PROSITE PS00989) SUPPORTS TRANSFER AP1S3 matches this signature (UniProt lists PROSITE PS00989 CLAT_ADAPTOR_S). It is a pan-AP-complex small-chain site, so the terms mapped from it are correspondingly general, but they are not wrong for any member. InterPro:IPR044733 · InterPro IPR044733, AP1_sigma (CDD cd14831) SUPPORTS TRANSFER This is the AP-1-sigma-specific signature, not a pan-AP one: AP1S3 matches cd14831 AP1_sigma. Terms mapped from it can legitimately name the AP-1 complex specifically. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt Belongs to the adaptor complexes small subunit family. PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0016192 vesicle-mediated transport | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | ACCEPT | Summary: ComplexPortal's statement that the sigma1C AP-1 variant mediates vesicle-mediated transport. Reason: The most basic true statement about this complex, and it agrees with the IBA and the InterPro mapping. The cited review is a weak source for it, but the claim is not in doubt and is supported by this gene's own primary literature. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0030117 membrane coat | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping placing AP1S3 as part of a membrane coat. Reason: Literally what the protein is: UniProt describes this entry as a component of the coat surrounding the cytoplasmic face of coated vesicles at the Golgi, and the GO definition of membrane coat explicitly includes coats formed by clathrin plus an adaptor complex. Generic, because the signature is generic, but exactly right. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR000804 · InterPro IPR000804, Clathrin adaptor complex small chain conserved site (PROSITE PS00989) SUPPORTS TRANSFER AP1S3 matches this signature (UniProt lists PROSITE PS00989 CLAT_ADAPTOR_S). It is a pan-AP-complex small-chain site, so the terms mapped from it are correspondingly general, but they are not wrong for any member. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0030121 AP-1 adaptor complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the AP-1-sigma-specific signature to the AP-1 adaptor complex. This is the single most solid annotation on the gene, and it now has direct structural proof. Reason: The GO definition of AP-1 adaptor complex names the sigma1 slot and states outright that the human complex is heterogeneric because sigma1A, sigma1B and sigma1C are encoded by different genes - so AP1S3 is part of this complex by the term's own definition. It is no longer only an inference: PDBe SIFTS maps chain S of the 2.34 A cryo-EM structure 7R4H to Q96PC3 residues 1-154 within an assembled, ARF1-activated AP-1 core, and UniProt's SUBUNIT statement lists AP1S3 as one of the three alternatives for the small adaptin. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR044733 · InterPro IPR044733, AP1_sigma (CDD cd14831) SUPPORTS TRANSFER This is the AP-1-sigma-specific signature, not a pan-AP one: AP1S3 matches cd14831 AP1_sigma. Terms mapped from it can legitimately name the AP-1 complex specifically. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt (sigma-type subunit AP1S1 or AP1S2 or AP1S3). file:human/AP1S3/AP1S3-uniprot.txt PDB; 7R4H; EM; 2.34 A; S=1-154. PMID:36261523 His-tagged AP-1β 1–584, GST-tagged AP-1γ 1–595, AP-1μ 1–423 and AP-1σ 1–154 were cloned into a pST44 vector and referred to as AP-1 core. file:human/AP1S3/AP1S3-bioinformatics/RESULTS.md PDBe SIFTS maps 7R4H chain S and 9DDT chain B to Q96PC3 (AP1S3) residues 1-154. |
| GO:0030121 AP-1 adaptor complex | NAS PMID:15377783 Crystal structure of the clathrin adaptor protein 1 core. | ACCEPT | Summary: ComplexPortal's composition statement for CPX-5049, the sigma1C variant of the ubiquitous AP-1 complex, cited to the AP-1 core crystal structure. Reason: Correct, and worth keeping alongside the InterPro row because it carries the named complex object: CPX-5049 is defined as AP1B1:AP1G1:AP1M1:AP1S3. The cited 2004 structure is of the mouse AP-1 core with sigma1A rather than sigma1C, so it establishes the architecture of the slot rather than AP1S3's occupancy of it; the occupancy is established directly by PDB 7R4H and 9DDT, both of which contain AP1S3 itself. Supporting Evidence: PMID:15377783 The AP-1 core comprises N-terminal fragments of the two large chains, beta1 and gamma, and the intact medium and small chains, micro1 and sigma1. file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. file:human/AP1S3/AP1S3-uniprot.txt PDB; 9DDT; X-ray; 1.68 A; B=1-154. |
| GO:0030659 cytoplasmic vesicle membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Automatic mapping of this entry's own UniProt cytoplasmic vesicle membrane location. Reason: UniProt asserts it on this entry, qualified as a peripheral membrane protein on the cytoplasmic side - which is precisely the topology of an adaptor coat subunit. Consistent with the Reactome rows for the same term. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0089 · UniProtKB Subcellular Location SL-0089 (Cytoplasmic vesicle membrane) SUPPORTS TRANSFER Asserted on this entry as a peripheral membrane protein on the cytoplasmic side of cytoplasmic vesicle membranes, which is exactly what an adaptor coat subunit is. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face |
| GO:0030659 cytoplasmic vesicle membrane | TAS Reactome:R-HSA-421835 | ACCEPT | Summary: Reactome places the AP-1 coat on the membrane of the vesicle being released from the TGN. Reason: The coat rides on the vesicle membrane from scission until uncoating; this agrees with UniProt's own subcellular-location assertion for the entry. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; |
| GO:0030659 cytoplasmic vesicle membrane | TAS Reactome:R-HSA-421836 | ACCEPT | Summary: Reactome's TGN-derived vesicle uncoating reaction has AP-1 on the vesicle membrane until it is shed. Reason: Same cycle as the scission row, and the same correct compartment. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle membrane; file:human/AP1S3/AP1S3-uniprot.txt Component of the coat surrounding the cytoplasmic face |
| GO:0032588 trans-Golgi network membrane | IEA GO_REF:0000117 | ACCEPT | Summary: An ARBA machine-learned rule conferring trans-Golgi network membrane. The rule is a grab-bag of ten unrelated condition sets, but the one that fires for AP1S3 is sigma-specific. Reason: Checked rather than waved through. ARBA00033972 confers exactly one annotation, GO:0032588, through ten condition sets spanning EF-hand, protein-kinase, ARM-repeat and other unrelated FunFams. Condition set 9 is the one that matches this protein: FunFam 3.30.450.60:FF:000005 plus taxon Catarrhini, and 3.30.450.60:FF:000005 is exactly the FunFam UniProt assigns to this entry ('AP complex subunit sigma'). So the match is to the sigma fold family, not an incidental hit, and the conferred location is the central AP-1 compartment, independently asserted by Reactome, ComplexPortal and the primary literature. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00033972 · ARBA00033972 (machine-learned rule conferring GO:0032588) SUPPORTS TRANSFER The rule has ten unrelated condition sets. The one that fires for AP1S3 is condition set 9: FunFam 3.30.450.60:FF:000005 plus taxon Catarrhini, and 3.30.450.60:FF:000005 is exactly the FunFam UniProt assigns to this entry ('AP complex subunit sigma'). The matching condition is sigma-specific rather than an incidental fold match. Supporting Evidence: file:human/AP1S3/AP1S3-uniprot.txt FunFam; 3.30.450.60:FF:000005 PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. PMID:15377783 We report the crystal structure of the core of the AP-1 complex, which functions in the trans-Golgi network (TGN). |
| GO:0032588 trans-Golgi network membrane | NAS PMID:15377783 Crystal structure of the clathrin adaptor protein 1 core. | ACCEPT | Summary: ComplexPortal assigns the trans-Golgi network membrane to CPX-5049, citing the AP-1 core structure paper, which states that AP-1 functions in the TGN. Reason: The cited paper says so in its own abstract, and the TGN is the defining AP-1 compartment. The structure is of the mouse sigma1A-containing core, so the statement is complex-level rather than sigma-1C-specific, but the location is not paralogue-dependent: the same paper attributes TGN localisation to ARF1 and PI-4-P, and localises the phosphoinositide determinant to a corner of the gamma chain, not to the sigma slot. Supporting Evidence: PMID:15377783 We report the crystal structure of the core of the AP-1 complex, which functions in the trans-Golgi network (TGN). PMID:15377783 TGN localization of AP-1 depends on the small GTPase, Arf1, and the phosphoinositide, PI-4-P. PMID:15377783 directed mutations of residues at a particular corner of the gamma chain prevent recruitment to the TGN in cells file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. |
| GO:0032588 trans-Golgi network membrane | TAS Reactome:R-HSA-2130641 | ACCEPT | Summary: Reactome's translocation of the TGN-lysosome vesicle places the AP-1 coat at the trans-Golgi network membrane. Reason: The TGN membrane is where AP-1 is recruited and where cargo is captured, so this is a core rather than incidental location. Supporting Evidence: PMID:36261523 The most prominent adaptor protein complex that is involved in cargo shuttling from the TGN to endolysosomes is AP-1 PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0032588 trans-Golgi network membrane | TAS Reactome:R-HSA-2213236 | ACCEPT | Summary: Reactome's TGN-lysosome vesicle uncoating reaction also lists the trans-Golgi network membrane. Reason: Same compartment, same well-supported claim. Supporting Evidence: PMID:36261523 The most prominent adaptor protein complex that is involved in cargo shuttling from the TGN to endolysosomes is AP-1 |
| GO:0032588 trans-Golgi network membrane | TAS Reactome:R-HSA-5333658 | ACCEPT | Summary: Reactome's CLAT:AP1:CLVS bind PI(3,5)P2 reaction places the clathrin/AP-1 coat at the trans-Golgi network membrane. Reason: Phosphoinositide binding is how the AP-1 coat is held on TGN and endosomal membranes, and the AP-1 core structure paper showed directly that mutating a particular corner of the gamma chain prevents TGN recruitment in cells while sparing ARF1-dependent liposome binding. Correct location. Supporting Evidence: PMID:15377783 TGN localization of AP-1 depends on the small GTPase, Arf1, and the phosphoinositide, PI-4-P. PMID:15377783 directed mutations of residues at a particular corner of the gamma chain prevent recruitment to the TGN in cells PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. |
| GO:0032588 trans-Golgi network membrane | TAS Reactome:R-HSA-8951498 | ACCEPT | Summary: Reactome's dissociation of the Arf1:GDP, AP-1 clathrin-coated nonameric complex is placed at the trans-Golgi network membrane. Reason: The ARF1-dependent recruitment and release cycle happens on this membrane; the ARF1-bound state of that cycle is the one captured in PDB 7R4H with AP1S3 as the sigma chain. Supporting Evidence: PMID:24791904 AP-1 is involved in the transport of cargoes between the trans -Golgi network and the endosomes, a process that requires the formation of specialized clathrin-coated vesicles. file:human/AP1S3/AP1S3-uniprot.txt PDB; 7R4H; EM; 2.34 A; S=1-154. |
| GO:0035615 clathrin-cargo adaptor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the AP-1-sigma signature to clathrin-cargo adaptor activity. This is the right molecular function for the protein, and the sigma subunit is the part of AP-1 that actually reads the cargo's sorting signal. Reason: The mapping is correct and, unusually for an IEA, it is now backed by structure at the residue level on this exact protein. In PDB 7R4H the sigma chain is AP1S3 (SIFTS: chain S = Q96PC3 1-154), and the cargo's acidic dileucine motif is read by AP1S3's own side chains - L65, F67, H85, V88 and V98 receive the two bulky motif residues, while K60 and R61 read a phosphoserine just downstream. The independent 1.68 A structure 9DDT shows the assembly chaperone AAGAB occupying that same Y62/V88/V98 pocket and sterically clashing with cargo peptides, which is a second, orthogonal demonstration that this is the cargo site. Two caveats recorded rather than acted on: the GO definition of this term says 'responsible for the formation of endocytic vesicles', which is AP-2 language and does not fit an AP-1 subunit, yet GO applies the term across AP-1 subunits (AP1G1, AP1M1 and AP1M2 all carry it by IBA or IDA) - the definition is what needs revising, not this annotation; and the sigma subunit supplies the cargo pocket but does not itself bridge to clathrin, so at the level of the whole activity AP1S3 contributes to rather than independently enables it, which is how it is recorded in core_functions. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR044733 · InterPro IPR044733, AP1_sigma (CDD cd14831) SUPPORTS TRANSFER This is the AP-1-sigma-specific signature, not a pan-AP one: AP1S3 matches cd14831 AP1_sigma. Terms mapped from it can legitimately name the AP-1 complex specifically. Supporting Evidence: PMID:36261523 STING L364 and I365 of the EXXXLI sorting motif engage L65, F67, H85, V88 and V98 of the σ subunit through hydrophobic interactions PMID:36261523 the phospho-moiety on S366 makes hydrogen bonds with a conserved basic patch formed by K60 and R61 of the σ subunit PMID:40752490 The dileucine motif binds to the σ subunit in an extended conformation, with the two leucines fitting in two adjacent hydrophobic pockets. PMID:40752490 the aromatic side chain of F153 fits into a hydrophobic pocket lined by Y62, V88, and V98 in AP1σ3 PMID:40752490 Superposing our AAGAB psGD:AP1σ3 structure with AP1 or AP2 σ subunit loaded with cargo peptides immediately reveals steric clashes between the AAGAB psGD and the cargo peptides file:human/AP1S3/AP1S3-bioinformatics/RESULTS.md 22 of 23 published positions resolve to exactly the residue named, in AP1S3's own numbering |
| GO:0060155 platelet dense granule organization | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: ComplexPortal assigns platelet dense granule organization to the sigma1C AP-1 variant, on the strength of a review in which AP-1 is one of several complexes redirected by Rab32/Rab38. Reason: Real AP-1 biology, but inherited by the sigma1C complex by definition rather than by experiment. The cited review makes an AP-1-complex-level statement about lysosome-related organelle biogenesis and contains no sigma-1C experiment; platelet dense granules form in megakaryocytes, and nothing in the record tests whether the sigma1C form of AP-1 is the one used there. Keep, because the complex genuinely participates and AP1S3 is a bona fide constituent of one of its variants, but this is not what AP1S3 is for. Supporting Evidence: PMID:23247405 redirect the ubiquitous machinery-BLOC-2, AP-1 and AP-3-to traffic specialized cargoes to melanosomes in melanocytes PMID:23247405 Lysosome-related organelles are found in specialized cell types such as melanocytes, platelets, lung alveolar type II cells and some innate and adaptive immune cells file:human/AP1S3/AP1S3-uniprot.txt ComplexPortal; CPX-5049; Ubiquitous AP-1 Adaptor complex, sigma1c variant. |
| GO:1903232 melanosome assembly | NAS PMID:23247405 Cell type-specific Rab32 and Rab38 cooperate with the ubiqui... | KEEP AS NON CORE | Summary: ComplexPortal likewise assigns melanosome assembly to the sigma1C AP-1 variant. Reason: The same inheritance, with the same gap. Melanosomes are built in melanocytes, and the cited review's claim is that Rab32 and Rab38 redirect the ubiquitous BLOC-2, AP-1 and AP-3 machinery to them - a statement about AP-1 as a complex. Whether the sigma1C variant is the one melanocytes use has not been asked. Defensible as a non-core, cell-type-restricted role of the complex AP1S3 belongs to. Supporting Evidence: PMID:23247405 Rab32 and Rab38 have both redundant and unique roles in the trafficking of melanin-producing enzymes and overall melanosome biogenesis PMID:23247405 redirect the ubiquitous machinery-BLOC-2, AP-1 and AP-3-to traffic specialized cargoes to melanosomes in melanocytes PMID:23247405 Lysosome-related organelles are found in specialized cell types such as melanocytes, platelets, lung alveolar type II cells and some innate and adaptive immune cells |
| GO:0005198 structural molecule activity | IC PMID:24791904 AP1S3 mutations are associated with pustular psoriasis and i... | NEW | Summary: Sigma-1C is a structural subunit of the AP-1 heterotetramer: it holds an interface with the medium adaptin, and the two pustular-psoriasis variants act by destabilising the protein or that interface rather than by changing what the complex selects. Reason: Inferred by curator from this gene product's own complex-membership annotation (GO:0030121 AP-1 adaptor complex), which is itself now established by two structures containing AP1S3. The inference rests on three independent lines. First, position: in the assembled core AP1S3 is the small chain packed against the medium adaptin, and the disease variant Arg33Trp sits precisely at that sigma-1C/mu-1A interface. Second, stability: the Phe4Cys variant, which lies in the hydrophobic core, reduces the amount of sigma-1C protein recovered after transfection into two cell lines, and the free subunit is largely misfolded when expressed on its own in bacteria, becoming a well-folded 1:1 species only when co-expressed with the AAGAB chaperone. Third, generality: sigma subunits have been shown to be required for AP-complex stability, with AP-2 used as the model because its sigma is encoded by a single gene. This is the only subunit-level molecular function GO can currently express for this protein; the activity one would rather state - binding the dileucine sorting signal - has no GO term, which is recorded here as a knowledge gap and a proposed new term. Propagation Review Root cause: NO FAILURE CORE Sources checked: GO:0030121 · AP-1 adaptor complex - this gene product's own complex-membership annotation, used as the IC basis SUPPORTS TRANSFER Worth stating plainly: on AP1S3 this basis term is itself carried only by IEA (InterPro IPR044733) and NAS (ComplexPortal) rows, so the inference is not resting on an experimental GOA annotation. What carries it is that two solved structures contain AP1S3 as the small chain of an assembled AP-1 core - 7R4H chain S and 9DDT chain B, both mapped to Q96PC3 1-154 by PDBe SIFTS - together with the demonstration that sigma subunits are required for AP-complex stability. Supporting Evidence: PMID:24791904 Given that AP-1 subunit σ1C is one of the core subunits thought to stabilize AP-1 heterotetramers PMID:24791904 Arg33 is critically located at the AP-1 σ1C/μ1A interface PMID:24791904 we observed decreased levels of the p.Phe4Cys protein upon transfection of mutant and wild-type (WT) constructs into human embryonic kidney 293 (HEK293) and HaCaT cells PMID:18428203 we demonstrated that sigma subunits are essential for the stability of human AP complexes PMID:40752490 Yet this small amount of σ subunit was mostly misfolded PMID:40752490 Both the elution position and the SDS-PAGE of SEC peak fractions suggest a 1:1 stoichiometry between AAGAB psGD and AP1σ3 |
| GO:0000045 autophagosome assembly | IMP PMID:27388993 AP1S3 Mutations Cause Skin Autoinflammation by Disrupting Ke... | NEW | Summary: AP1S3 loss reduces starvation-induced autophagosome formation in two independent cell backgrounds, and the defect is rescued by wild-type but not by the pustular-psoriasis p.Arg33Trp protein. Reason: Missing from GOA, and well evidenced in both perturbation directions. Loss: stable shRNA knockdown in HaCaT keratinocytes significantly reduced LC3-II, and an independent CRISPR-Cas9 knockout in HEK293 reproduced the decrease in starvation-induced LC3-II, with fewer LC3-GFP-positive autophagosomes by microscopy. Gain: re-expression of wild-type AP1S3 restored the phenotype while the p.Arg33Trp disease allele did not, which both confirms direction and ties the process to the protein rather than to an off-target effect of the guide or hairpin. The mechanism is complex-level and indirect - the authors' premise is that autophagosome formation requires a functional AP-1 complex - so this is an involved_in process claim about AP-1-dependent membrane traffic, not a claim that AP1S3 is core autophagy machinery. Note that the knockout background was HEK293, not a keratinocyte, so the autophagy requirement is not keratinocyte-restricted; only the downstream inflammatory consequence (p62 accumulation, NF-kB activation, IL-36-alpha overexpression) was characterised in keratinocytes. Supporting Evidence: PMID:27388993 We found that LC3-II levels were significantly reduced in AP1S3 knockdown versus control cell lines PMID:27388993 AP1S3 silencing causes a very significant decrease in starvation-induced LC3-II accumulation PMID:27388993 we used fluorescence microscopy to visualize the expression of LC3-green fluorescent protein (GFP) constructs transfected into the HEK293 AP1S3 knockout cell line PMID:27388993 This phenotype was rescued by the overexpression of wild-type but not mutant (p.Arg33Trp) AP1S3 constructs PMID:27388993 Because autophagosome formation requires a functional AP-1 complex PMID:27388993 We found that AP1S3 knockout disrupts keratinocyte autophagy, causing abnormal accumulation of p62, an adaptor protein mediating NF-κB activation. |
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Download this section (compressed HTML)Q: Is there any cargo whose AP-1-dependent sorting requires sigma-1C specifically, or are the three sigma-1 paralogues interchangeable at the level of cargo selection with only their abundance differing between tissues?
Suggested experts: Francesca Capon, Peter Schu
Q: In cells, which sigma-1 paralogue delivers the AP-1-dependent termination of STING signalling? The 2.34 A structure used sigma-1C, but the knockdowns and sigma point mutants in the same study used sigma-1A.
Suggested experts: Andrea Ablasser, James H. Hurley
Q: Does the AAGAB pseudoGTPase domain compete with cargo for the sigma subunit in cells, so that free AAGAB sets how much cargo-competent AP-1 exists, or is the chaperone released before the tetramer ever sees a sorting motif?
Suggested experts: Qian Yin, Jingshi Shen
Q: Do the pustular psoriasis variants Phe4Cys and Arg33Trp reduce the amount of assembled AP-1 without changing which cargoes it selects, as their positions outside the cargo surface predict?
Suggested experts: Francesca Capon, Satveer K. Mahil
Experiment: Generate keratinocytes null for each sigma-1 gene singly and in combination, then compare the AP-1 cargo repertoire by proximity labelling of the gamma subunit followed by quantitative mass spectrometry. Complement each null line with each of the three paralogues in turn and score both the cargo repertoire and the TLR3 endosomal-delivery and starvation-induced LC3-II phenotypes. Interchangeability predicts full cross-rescue at matched protein levels.
Hypothesis: The three sigma-1 paralogues are interchangeable for cargo selection, and the epidermal specificity of AP1S3 loss reflects relative abundance rather than specificity.
Type: proximity labelling proteomics with paralogue swap complementation
Experiment: Measure the affinity of a recombinant gamma/sigma-1C hemicomplex for synthetic peptides carrying a [DE]XXXL[LI] motif, phosphorylated and unphosphorylated, by isothermal titration calorimetry or bio-layer interferometry. Compare wild-type sigma-1C with V88D, I103S and K60A/R61A - the substitutions previously made only in sigma-1A - and with the disease variants F4C and R33W. The prediction is that the pocket mutants lose peptide binding while F4C and R33W do not, separating cargo selectivity from complex assembly.
Hypothesis: AP1S3 binds cargo dileucine motifs directly, through the pockets identified in PDB 7R4H, and the pustular psoriasis variants do not affect that binding.
Type: quantitative peptide binding with structure-guided mutagenesis
Experiment: Use the AAGAB psGD:AP1S3 interface mutants already characterised (AAGAB 2YR and DFEAV5R) to titrate chaperone occupancy in cells, and measure in parallel the amount of assembled AP-1, the surface transferrin receptor, and dileucine-cargo capture. A competition model predicts that partial loss of AAGAB binding lowers assembled AP-1 without lowering per-complex cargo affinity, while an occlusion model predicts free cargo-competent sigma rises transiently.
Hypothesis: AAGAB binding and cargo binding are mutually exclusive on sigma-1C, so AAGAB gates the cargo-competent pool of AP-1.
Type: structure-guided interface mutagenesis with cell-surface cargo assay
Experiment: In AP1S3-null HEK293 and keratinocytes, track ATG9A itinerary by live imaging and surface-biotinylation and ask whether restoring ATG9A delivery to the autophagosome-initiation compartment - for example by an ATG9A construct whose sorting is made AP-1-independent - rescues starvation-induced LC3-II without restoring AP1S3. Rescue would place AP1S3 upstream in membrane supply rather than in the autophagy machinery itself.
Hypothesis: The autophagy defect of AP1S3-null cells is a consequence of mis-sorted AP-1 cargo rather than of a direct role in autophagosome biogenesis.
Type: cargo-itinerary imaging with sorting-independent rescue construct
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: No GO term expresses the one molecular activity the AP-complex sigma subunit performs by itself - binding the [DE]XXXL[LI] dileucine sorting signal of a cargo tail - so the best available annotation for AP1S3 is either a complex-level term it only contributes to or a bare protein binding row.
OPEN ONTOLOGY MF_DARK
What is known: The activity itself is not in doubt and is resolved at 2.34 A on AP1S3 itself: the motif's two bulky residues sit in adjacent hydrophobic pockets formed by Leu65, Phe67, His85, Val88 and Val98, with Lys60/Arg61 reading an adjacent phosphoserine. GO already has the tyrosine-motif counterpart (GO:0089710) and the complex-level clathrin-cargo adaptor activity (GO:0035615). Only the dileucine term is missing.
Significance: The gap is family-wide, not AP1S3-specific: every sigma subunit of AP-1, AP-2 and AP-4 has the same site and the same missing term, which is part of why these proteins accumulate uninformative protein binding annotations.
What would resolve it: Create the proposed term as a sibling of GO:0089710 under protein binding, and separately revise the definition of GO:0035615, which currently says the activity is 'responsible for the formation of endocytic vesicles' even though GO applies the term to AP-1 subunits acting at the trans-Golgi network.
Provenance (the field's own admissions):
Gap: No cargo is known that the sigma-1C form of AP-1 selects and the sigma-1A or sigma-1B forms do not, so it is not established that AP1S3 has any biological process of its own as opposed to inheriting the complex's.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: It is established that the three sigma-1 paralogues are largely redundant in peripheral tissues, that they are not wholly interchangeable in neurons (sigma-1A and sigma-1B regulate early endosome maturation differently), and that AP1S3 is the one whose loss produces an epidermal phenotype. What is missing is the cargo that explains the difference.
Significance: This is the question that decides whether AP1S3 deserves process annotations distinct from the AP-1 complex's, and whether the pustular psoriasis phenotype is a dosage effect or a specificity effect.
What would resolve it: A comparative proteomic screen of AP-1 cargo in cells expressing only one sigma-1 paralogue at a time would either name the selective cargo or establish that the difference is quantitative.
Provenance (the field's own admissions):
Gap: Why loss of a broadly expressed, functionally redundant subunit produces a phenotype confined to the skin is unresolved; the proposed explanation - relative abundance in keratinocytes plus an IL-36 amplification loop - has not been tested by restoring the other paralogues.
NARROWING BIOLOGY BP_DARK
What is known: The downstream circuit is well characterised: loss of AP1S3 impairs autophagy, p62 accumulates, NF-kappa-B is activated, IL-36-alpha rises, and IL-36 blockade normalises the cytokine profile in patient keratinocytes. Expression data show the transcript is abundant in keratinocytes and scarce in neutrophils and CD4+ T cells, while UniProt describes the gene overall as widely expressed.
Significance: Tissue-restricted phenotypes from ubiquitously expressed trafficking genes are a recurring puzzle in this family - AP1S1 causes MEDNIK and AP1S2 an X-linked intellectual disability syndrome - and AP1S3 is the most tractable case because the effector cytokine is druggable.
What would resolve it: Quantify the three sigma-1 proteins (not transcripts) across keratinocytes, neurons and enterocytes, and test whether ectopic sigma-1A or sigma-1B rescues the autophagy and IL-36 phenotypes of AP1S3-null keratinocytes.
Provenance (the field's own admissions):
Gap: Which sigma-1 paralogue serves the AP-1-dependent termination of STING signalling is not established, because the structural and the loss-of-function halves of that work used different paralogues.
OPEN BIOLOGYCURATION BP_DARK
What is known: The recognition chemistry is settled: activated STING's C-terminal tail presents an EXXXLI motif plus a TBK1-phosphorylated serine, and the structure resolving that interaction contains AP1S3 as the sigma chain. What is not settled is whether AP1S3 is the paralogue that does this in cells - the knockdowns and the sigma point mutants in the same study were AP1S1.
Significance: If AP1S3 does serve this pathway, the loss-of-interferon phenotype of AP1S3 knockdown would have two independent routes - failure to deliver TLR3 and failure to terminate STING - which bears directly on how the disease variants act.
What would resolve it: Single-paralogue knockouts assayed for STING degradation kinetics, with rescue by each sigma-1 in turn. No process annotation for STING or type I interferon is proposed for AP1S3 until that is done.
Provenance (the field's own admissions):
Gap: Nothing is known about isoform-specific function, even though the MANE-Select transcript encodes isoform 4 rather than the UniProt canonical isoform 1, and no GO annotation on this gene is isoform-qualified.
OPEN BIOLOGYCURATION CC_DARK
What is known: Four isoforms are annotated; two of them, isoforms 2 and 3, carry premature stop codons and are expected to be degraded by nonsense-mediated decay. Isoforms 1 and 4 differ only in their last eleven residues, a region that in the AP-1 core makes minimal contact with the other subunits and is unmodelled in PDB 9DDT. Both published structures used isoform 1.
Significance: If isoform 4 is the dominant transcript, every functional statement about this protein rests on a sequence that may not be the one cells mostly make, even though the divergent segment is peripheral to the fold.
What would resolve it: Isoform-resolved proteomics or long-read transcript quantification in keratinocytes, followed by a side-by-side complementation test of isoforms 1 and 4 in AP1S3-null cells.
Provenance (the field's own admissions):
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