ATP6V1D encodes the D subunit (28 kDa) of the V1 peripheral sector of the vacuolar-type H+-ATPase (V-ATPase). Subunit D forms the central rotor of V1 together with subunit F; ATP hydrolysis by the catalytic A3B3 hexamer drives rotation of the D-F stalk, which is mechanically coupled to the V0 proteolipid c-ring to translocate protons across organelle membranes. The human V-ATPase complex is responsible for acidifying lysosomes, endosomes, the Golgi apparatus, and other intracellular compartments, and in specialized cell types for extracellular acidification at the plasma membrane. Beyond proton pumping, the V1 D subunit directly contacts the Ragulator scaffold on lysosomes, and V-ATPase activity is required for amino acid-sensitive mTORC1 activation via an inside-out signaling mechanism. ATP6V1D additionally interacts with SNX10 and localizes to the centrosome and cilium base, where the V-ATPase is required for ciliogenesis. The protein is ubiquitously expressed in human tissues.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0033176 proton-transporting V-type ATPase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATP6V1D is part of the V-type ATPase complex. Confirmed by cryo-EM structure and biochemical data. Reason: The D subunit is a core structural and functional component of the V1 sector of the V-type ATPase complex. Multiple lines of evidence including cryo-EM (PMID:33065002) and biochemical pulldowns (PMID:18752060) confirm complex membership. Supporting Evidence: PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. file:human/ATP6V1D/ATP6V1D-uniprot.txt Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons |
| GO:0007035 vacuolar acidification | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATP6V1D participates in vacuolar acidification. Well-supported by the established role of V-ATPase in acidifying intracellular compartments. Reason: The V-ATPase is the primary driver of organellar acidification in eukaryotes, and subunit D is a core structural component essential for complex function. Vacuolar acidification is the core biological process. Supporting Evidence: PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. PMID:32001091 V-ATPases are membrane-embedded protein complexes that function as ATP hydrolysis-driven proton pumps. V-ATPases are the primary source of organellar acidification in all eukaryotes, making them essential for many fundamental cellular processes. |
| GO:0046961 proton-transporting ATPase activity, rotational mechanism | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that subunit D contributes to proton-transporting ATPase activity via rotational mechanism. Supported by the established central rotor function of subunit D in the rotary mechanism. Reason: Subunit D is a core structural component of the V1 central rotor that directly participates in the rotary mechanism. The contributes_to qualifier is appropriate since this is a complex-level activity. Supporting Evidence: PMID:18752060 Energy from this reaction drives the rotation of a central stalk consisting of V1 subunits D and F and this is coupled to rotation of the V0 proteolipid ring made up of c, c′ and c″. PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. |
| GO:0005765 lysosomal membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location vocabulary mapping. Well-supported by multiple independent HDA and IDA lysosomal membrane annotations. Reason: Lysosomal membrane is the primary functional location of the V-ATPase complex. Supported by HDA proteomics (PMID:17897319) and IDA data (PMID:22053050). |
| GO:0005813 centrosome | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular location vocabulary mapping based on the centrosome localization reported in PMID:21844891. Reason: Centrosome localization of ATP6V1D (via SNX10 interaction) is supported by IDA evidence (PMID:21844891) but represents a secondary ciliogenesis-related function rather than the core lysosomal proton-pumping role. Supporting Evidence: PMID:21844891 SNX10 interacts with V-ATPase complex and targets it to the centrosome where ciliogenesis is initiated. |
| GO:0005929 cilium | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular location vocabulary mapping based on cilium localization reported in PMID:21844891. Reason: Cilium localization is supported by IDA evidence but represents a secondary ciliogenesis-related function. The V-ATPase participates in ciliogenesis via vesicular trafficking to the cilium base. Supporting Evidence: PMID:21844891 Like SNX10, V-ATPase regulates ciliogenesis in vitro and in vivo and does so synergistically with SNX10. We further discover that SNX10 and V-ATPase regulate the ciliary trafficking of Rab8a, which is a critical regulator of ciliary membrane extension. |
| GO:0016020 membrane | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Generic membrane localization from UniProt vocabulary mapping. The V1 D subunit associates with the cytoplasmic face of membranes as part of the V-ATPase complex. Reason: The generic membrane term is subsumed by the more specific lysosomal membrane, Golgi membrane, and endosome membrane annotations. The IDA annotation from PMID:18752060 (membrane) is more specific in context and provides better granularity. |
| GO:0030665 clathrin-coated vesicle membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular location vocabulary mapping based on ortholog data. V-ATPase functions on clathrin-coated vesicles for endocytic pathway acidification. Reason: The clathrin-coated vesicle membrane localization is consistent with V-ATPase's broad role in acidifying endocytic vesicles, but is not the primary functional context for this subunit. |
| GO:0046961 proton-transporting ATPase activity, rotational mechanism | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation. The enables qualifier for the whole-complex activity is somewhat imprecise for a structural subunit, but the rotational ATPase activity is the core molecular function. Reason: The proton-transporting ATPase activity via rotational mechanism is the core molecular function of the complex in which ATP6V1D is an indispensable structural component. The IBA annotation with contributes_to is more precise, but this IEA is consistent. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Generic protein binding from a large-scale human interactome proteome map. Not informative for the specific function of ATP6V1D. Reason: Protein binding is uninformative for this V-ATPase subunit. A high-throughput interactome map does not establish a meaningful GO annotation for ATP6V1D core function. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Generic protein binding from a reference human binary protein interactome map. High-throughput; not informative. Reason: Protein binding from high-throughput interactome studies lacks specificity and is not useful for understanding ATP6V1D function. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Generic protein binding from a dual proteome-scale interactome network study. High-throughput; not informative. Reason: High-throughput interactome data should not be used to assert generic protein binding as a meaningful function for a structural V-ATPase subunit. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | MARK AS OVER ANNOTATED | Summary: Generic protein binding from the OpenCell endogenous tagging study. High-throughput; not informative for core function. Reason: Protein binding is uninformative for ATP6V1D; these high-throughput interaction data points do not reveal specific biological function. |
| GO:0015078 proton transmembrane transporter activity | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl ortholog-transfer annotation. Proton transmembrane transporter activity is the molecular function of the V-ATPase complex; subunit D contributes via the rotary mechanism. Reason: This is an appropriate annotation for a core V-ATPase structural subunit. The contributes_to qualifier correctly acknowledges that the molecular function belongs to the whole complex. |
| GO:0033176 proton-transporting V-type ATPase complex | IEA GO_REF:0000120 | ACCEPT | Summary: Automated IEA annotation consistent with the IBA and IDA evidence for complex membership. Reason: Redundant with IBA but consistent with cryo-EM structural evidence. |
| GO:0097401 synaptic vesicle lumen acidification | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl ortholog-transfer annotation for synaptic vesicle lumen acidification. V-ATPase acidifies synaptic vesicles to enable neurotransmitter loading. However, there is no direct evidence that the ubiquitous D subunit specifically functions in neuronal synaptic vesicles as opposed to other organelles. Reason: Synaptic vesicle lumen acidification is a legitimate biological process in which V-ATPase participates; the D subunit is a ubiquitously expressed component that would be present in neuronal V-ATPase complexes. However, this is a non-core context relative to lysosomal/endosomal function. |
| GO:0098850 extrinsic component of synaptic vesicle membrane | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl ortholog-transfer annotation placing the D subunit on synaptic vesicle membrane. The V1 peripheral sector is an extrinsic component of vesicle membranes. Reason: Supported by the V-ATPase's role in synaptic vesicle acidification, but this is non-core relative to the primary lysosomal/endosomal acidification function. |
| GO:0071230 cellular response to amino acid stimulus | IDA PMID:22053050 mTORC1 senses lysosomal amino acids through an inside-out me... | ACCEPT | Summary: Direct evidence from Zoncu et al. (2011) showing the V-ATPase (specifically the V1 domain including subunit D) is required for mTORC1 activation in response to amino acids. The V1 D subunit directly contacts the Ragulator complex, and amino acids regulate this interaction. Reason: The V-ATPase's role in amino acid sensing for mTORC1 is a genuine secondary function with direct experimental evidence. Subunit D specifically interacts with Ragulator p18 and p14 in vitro. This is well-supported functional biology beyond simple proton pumping. Supporting Evidence: PMID:22053050 the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. In a cell-free system, ATP hydrolysis by the v-ATPase was necessary for amino acids to regulate the v-ATPase-Ragulator interaction and promote mTORC1 translocation. PMID:22053050 the V1 component D with p18 and, to a lesser degree, with p14 (Fig. 3D). No direct interactions were detected between the Rag GTPases and purified v-ATPase subunits |
| GO:0160124 guanyl nucleotide exchange factor activator activity | IDA PMID:22053050 mTORC1 senses lysosomal amino acids through an inside-out me... | KEEP AS NON CORE | Summary: The V-ATPase contributes to GEF activator activity in the context of Ragulator-mediated Rag GTPase nucleotide exchange during amino acid signaling to mTORC1. The mechanistic link is that V-ATPase activity (ATP hydrolysis-driven rotation) is required to activate Ragulator as a GEF activator complex. Reason: This annotation reflects a genuine but secondary function of the V-ATPase complex in mTORC1 signaling. It is mechanistically supported but is not the primary proton-pump function of the complex. Supporting Evidence: PMID:22053050 amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal surface, the site of mTORC1 activation. We found that the vacuolar H(+)-adenosine triphosphatase ATPase (v-ATPase) is necessary for amino acids to activate mTORC1. |
| GO:0005765 lysosomal membrane | IDA PMID:22053050 mTORC1 senses lysosomal amino acids through an inside-out me... | ACCEPT | Summary: Direct experimental evidence from the Zoncu et al. (2011) study shows the V-ATPase is active at the lysosomal membrane for both proton pumping and amino acid-sensitive mTORC1 signaling. Reason: Lysosomal membrane is the primary site of V-ATPase function, and this IDA annotation from a key mechanistic study is well-supported. Supporting Evidence: PMID:22053050 the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. |
| GO:0046611 lysosomal proton-transporting V-type ATPase complex | IDA PMID:22053050 mTORC1 senses lysosomal amino acids through an inside-out me... | ACCEPT | Summary: Direct evidence from the Zoncu et al. (2011) study showing the V-ATPase complex on lysosomes; subunit D is part of this complex. Reason: Well-supported by both the amino acid sensing study (PMID:22053050) and the structural data (PMID:33065002). Supporting Evidence: PMID:22053050 the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. |
| GO:1904263 positive regulation of TORC1 signaling | IDA PMID:22053050 mTORC1 senses lysosomal amino acids through an inside-out me... | KEEP AS NON CORE | Summary: The V-ATPase is required for positive regulation of mTORC1 signaling by amino acids. Subunit D directly contacts Ragulator, and ATP hydrolysis is required for mTORC1 activation. This is a genuine secondary function. Reason: Positive regulation of TORC1 signaling is supported and real but is a secondary function of the V-ATPase complex, not the primary proton-pumping role. Supporting Evidence: PMID:22053050 ATP hydrolysis and the associated rotation of the v-ATPase appear to be essential to relay an amino acid signal from the lysosomal lumen to the Rag GTPases, whereas the capacity of the v-ATPase to set up the lysosomal proton gradient is dispensable. |
| GO:0005886 plasma membrane | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Immunofluorescence-based annotation. V-ATPase can be targeted to the plasma membrane in specialized cell types for extracellular acidification. Reason: Plasma membrane localization of V-ATPase is real in specialized contexts (osteoclasts, kidney intercalated cells, tumor cells) but is not the primary site of function for this ubiquitously expressed subunit. |
| GO:0000139 Golgi membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review (Vasanthakumar and Rubinstein 2020). V-ATPase acidifies the Golgi apparatus, and the D subunit is present as part of the complex. Reason: Golgi membrane localization is a well-established aspect of V-ATPase biology; Golgi acidification is required for proper glycosylation and protein trafficking. |
| GO:0005765 lysosomal membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Consistent with multiple other lysosomal membrane annotations. Reason: Core localization supported by multiple evidence types. |
| GO:0005886 plasma membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | KEEP AS NON CORE | Summary: NAS from V-ATPase review. Reason: Plasma membrane localization of V-ATPase is real in specialized contexts but is not the primary site for the ubiquitous D subunit. |
| GO:0007035 vacuolar acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Consistent with core V-ATPase function. Reason: Vacuolar acidification is the core biological process of V-ATPase. |
| GO:0007042 lysosomal lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Lysosomal lumen acidification is a specific, well-established aspect of V-ATPase function that is more precise than the broader vacuolar acidification term. Reason: Lysosomal lumen acidification is a core function of the V-ATPase. |
| GO:0007042 lysosomal lumen acidification | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study (Wang et al. 2020). Consistent with the established role of V-ATPase in lysosomal acidification. Reason: Supported by extensive V-ATPase biology. |
| GO:0010008 endosome membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. V-ATPase acidifies endosomes; the D subunit is present as part of the complex. Reason: Endosome membrane is an established location for V-ATPase function in the endocytic pathway. |
| GO:0016020 membrane | IDA PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | MARK AS OVER ANNOTATED | Summary: IDA from the human V-ATPase structural study (cryo-EM). The D subunit is part of the membrane-associated V-ATPase complex on the cytoplasmic face of membranes. Reason: The generic membrane annotation is subsumed by the more specific lysosomal membrane, Golgi membrane, and endosome membrane annotations. |
| GO:0033176 proton-transporting V-type ATPase complex | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study. Consistent with IDA from PMID:18752060 and IBA annotation. Reason: Well-supported complex membership. |
| GO:0048388 endosomal lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Endosomal lumen acidification by V-ATPase is a core function. Reason: Core function of V-ATPase in the endocytic pathway. |
| GO:0051452 intracellular pH reduction | NAS PMID:32001091 Structure and Roles of V-type ATPases. | MARK AS OVER ANNOTATED | Summary: NAS from V-ATPase review. Intracellular pH reduction is a core outcome of V-ATPase activity. This term is somewhat redundant with the more specific acidification terms. Reason: The intracellular pH reduction term is a less specific way to describe the same function captured by the more precise lysosomal/endosomal/Golgi lumen acidification annotations. Redundant and non-specific. |
| GO:0061795 Golgi lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. V-ATPase acidifies the Golgi lumen, which is important for glycosylation and protein sorting. Reason: Core function of V-ATPase in Golgi biology. |
| GO:1902600 proton transmembrane transport | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study. Proton transmembrane transport is the core molecular process performed by V-ATPase. Reason: Core biological process of V-ATPase. |
| GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain | ISS GO_REF:0000024 | ACCEPT | Summary: Ortholog-based annotation placing the D subunit in the V1 domain. Confirmed by human cryo-EM structural data. Reason: The D subunit is a defining structural component of the V1 domain, confirmed by cryo-EM. Supporting Evidence: PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. |
| GO:0005886 plasma membrane | TAS Reactome:R-HSA-6799350 | KEEP AS NON CORE | Summary: Reactome TAS annotation placing ATP6V1D in specific granule membrane of neutrophils. V-ATPase is present in neutrophil granules. Reason: Neutrophil-specific granule function is a non-core context for this ubiquitous subunit. |
| GO:0035579 specific granule membrane | TAS Reactome:R-HSA-6799350 | KEEP AS NON CORE | Summary: Reactome TAS annotation for V-ATPase in neutrophil specific granule membrane. Reason: Neutrophil-specific context; non-core for this ubiquitous subunit. |
| GO:0016241 regulation of macroautophagy | NAS PMID:22982048 Lipofuscin is formed independently of macroautophagy and lys... | MARK AS OVER ANNOTATED | Summary: NAS from a study on lipofuscin and macroautophagy (PMID:22982048). V-ATPase is required for lysosomal acidification, which is necessary for autophagosome-lysosome fusion and degradation. However, this is an indirect effect rather than a specific regulatory function. Reason: Regulation of macroautophagy is an indirect consequence of V-ATPase's role in lysosomal acidification. The annotation overstates the specificity; the core function is lysosomal proton pumping, not macroautophagy regulation per se. |
| GO:0033176 proton-transporting V-type ATPase complex | IDA PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | ACCEPT | Summary: Direct experimental evidence from Smith et al. (2008) demonstrating that human D subunit co-purifies with V-ATPase complex and directly interacts with central stalk components. Reason: The most specific experimental evidence for complex membership. Pulldown experiments demonstrated direct D-F and D-d subunit interactions. Supporting Evidence: PMID:18752060 each can pull down the central stalk's D and F subunits from human kidney membrane, and in vitro studies using D and F further showed that the interactions between these proteins and the d subunit is direct. |
| GO:0070062 extracellular exosome | HDA PMID:19199708 Proteomic analysis of human parotid gland exosomes by multid... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomics detection of ATP6V1D in parotid gland exosomes. V-ATPase subunits can co-purify with exosomes due to membrane association. Reason: Exosome detection by proteomics likely reflects membrane co-purification rather than a specific function of subunit D in exosomes. This is a non-core, likely artifactual localization for a primarily lysosomal/endosomal subunit. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomics detection in urinary exosomes. Same reasoning as the parotid gland exosome annotation. Reason: Urinary exosome proteomics detection likely reflects lysosomal membrane co-purification; not a specific function. |
| GO:0005765 lysosomal membrane | HDA PMID:17897319 Integral and associated lysosomal membrane proteins. | ACCEPT | Summary: Lysosomal membrane proteomics study detected ATP6V1D, confirming its lysosomal membrane localization. Reason: This direct proteomics evidence for lysosomal membrane localization is consistent with the established biology of V-ATPase. |
| GO:0061512 protein localization to cilium | IMP PMID:21844891 A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and... | KEEP AS NON CORE | Summary: The V-ATPase (including subunit D via SNX10 interaction) is required for proper localization of proteins to the cilium. V-ATPase knockout disrupts Rab8a ciliary trafficking. Reason: This is a genuine secondary function of the V-ATPase involving subunit D, but it is not the core lysosomal acidification function. Supporting Evidence: PMID:21844891 SNX10 and V-ATPase regulate the ciliary trafficking of Rab8a, which is a critical regulator of ciliary membrane extension. |
| GO:0005515 protein binding | IPI PMID:21844891 A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and... | MARK AS OVER ANNOTATED | Summary: The interaction detected in PMID:21844891 is the specific SNX10-V-ATPase interaction; however, the annotation is recorded as generic protein binding rather than the informative SNX10 interaction. Reason: Protein binding is uninformative; the underlying interaction with SNX10 is more informative. The generic protein binding term should be replaced if a more specific term exists. As no specific SNX10-binding GO term exists, this is best flagged as over-annotated. |
| GO:0005813 centrosome | IDA PMID:21844891 A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and... | KEEP AS NON CORE | Summary: Direct experimental evidence (IDA) showing ATP6V1D colocalizes with centrosome marker proteins, mediated by SNX10 interaction that targets V-ATPase to the centrosome. Reason: Centrosome colocalization is experimentally supported but is a secondary ciliogenesis-related function. Supporting Evidence: PMID:21844891 SNX10 interacts with V-ATPase complex and targets it to the centrosome where ciliogenesis is initiated. |
| GO:0005929 cilium | IDA PMID:21844891 A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and... | KEEP AS NON CORE | Summary: Direct evidence that V-ATPase (including D subunit) colocalizes with cilium. Reason: Secondary ciliogenesis function. |
| GO:0060271 cilium assembly | IMP PMID:21844891 A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and... | KEEP AS NON CORE | Summary: V-ATPase loss-of-function (through V-ATPase subunit knockdown including components targeting D subunit's complex) impairs cilium assembly in vitro and in vivo. Reason: Cilium assembly is a genuine secondary function of the V-ATPase complex, supported by IMP evidence, but is not the primary lysosomal acidification role. Supporting Evidence: PMID:21844891 V-ATPase regulates ciliogenesis in vitro and in vivo and does so synergistically with SNX10. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-1222516 | KEEP AS NON CORE | Summary: Reactome TAS annotation placing ATP6V1D in cytosol, consistent with the V1 domain being a peripheral complex on the cytoplasmic face of membranes. Reason: The V1 peripheral sector, including subunit D, is present in the cytosol as a soluble complex during regulated disassembly from V0. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-5252133 | KEEP AS NON CORE | Summary: Additional Reactome TAS annotation for cytosol localization. Reason: Same reasoning as above; the V1 domain can exist in cytosol. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-74723 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent with V1 domain biology. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-917841 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent with V1 domain biology. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9639286 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol in RRAG-related pathway context. Reason: V-ATPase participates in mTORC1 signaling on lysosomal surface, with V1 components accessible from cytosol. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640167 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640168 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640175 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640195 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9645598 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9645608 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9646468 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005515 protein binding | IPI PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | MARK AS OVER ANNOTATED | Summary: The IPI protein binding annotation from PMID:18752060 reflects specific interactions of subunit D with the V0 d subunit and with subunit F, which are mechanistically important. However, the generic protein binding term is less informative than the established subunit interactions. Reason: The specific interactions (D-F central stalk; D-d1/d2 rotor junction) are more meaningful than a generic protein binding annotation. No specific binding term exists for the D-F or D-d interactions, but protein binding is uninformative here. |
| GO:0016020 membrane | IDA PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | MARK AS OVER ANNOTATED | Summary: IDA from Smith et al. (2008) showing D subunit in membrane preparations. The D subunit is a peripheral membrane protein on the cytoplasmic face. Reason: The generic membrane annotation is subsumed by the more specific lysosomal membrane and other organelle membrane annotations. |
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Download this section (compressed HTML)Q: Is the role of subunit D in the Ragulator interaction specific to this subunit, or shared by other V1 subunits? What is the structural basis of D-Ragulator binding?
Q: Do disease-causing mutations in V-ATPase subunits affect the D-F central stalk interactions, and if so, does this impair ciliogenesis in addition to acidification?
Q: What is the mechanism by which SNX10-V-ATPase targeting to the centrosome promotes ciliogenesis? Is this dependent on V-ATPase proton-pumping activity or structural interactions?
Experiment: Cryo-EM structure determination of the V-ATPase-Ragulator complex to define the D subunit contact interface with p18 and p14, and to identify amino acid-dependent conformational changes.
Hypothesis: The D subunit directly contacts Ragulator at the lysosomal surface and this interface can be structurally defined.
Type: structural biology
Experiment: Engineer separation-of-function mutations in ATP6V1D that disrupt the Ragulator interaction without affecting V-ATPase proton pumping activity, then test mTORC1 activation in response to amino acids.
Hypothesis: The D-Ragulator contact can be uncoupled from proton pumping by targeted mutations.
Type: mutagenesis and functional assay
Experiment: Time-lapse imaging of fluorescently tagged V-ATPase-SNX10 complex during ciliation initiation; test whether V-ATPase proton-pumping activity or only its structural association with SNX10 is required for ciliogenesis.
Hypothesis: V-ATPase targeting to the centrosome by SNX10 is required for ciliogenesis and occurs during a specific window of ciliation initiation.
Type: live cell imaging and genetic rescue
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