{"gene":"VPS33A","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2013,"finding":"Crystal structure of human VPS33A confirmed its identity as a Sec1/Munc18 (SM) family member; VPS16 residues 642-736 are necessary and sufficient to recruit VPS33A to the HOPS complex; mutations at the VPS33A-VPS16 binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.","method":"X-ray crystallography, in vitro binding assays, mutagenesis, cell-based rescue experiments","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus mutagenesis validated in vitro and in cells","pmids":["23901104"],"is_preprint":false},{"year":2015,"finding":"VPS33A is recruited to the HOPS complex via its interaction with VPS16; VPS16/VPS33A interface mutants that abolish binding fail to rescue lysosome fusion with endosomes or autophagosomes; the entire HOPS complex (including VPS33A) is required for endosome-lysosome and autophagosome-lysosome fusion, whereas the paralogous VPS33B/VIPAR complex is not.","method":"Crystal structure-guided mutagenesis, siRNA depletion, fluorescent dextran delivery assay, immunoprecipitation","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 1-2 — structure-guided mutagenesis combined with functional rescue and orthogonal trafficking assays","pmids":["25783203"],"is_preprint":false},{"year":2003,"finding":"VPS33A is a mammalian Sec1-family protein orthologous to yeast Vps33 and Drosophila carnation; loss-of-function (buff mouse point mutation) causes defective biogenesis of lysosomes, melanosomes, and storage granules, identifying VPS33A as the first mammalian component of the class C vacuole/prevacuole-associated t-SNARE complex.","method":"Positional cloning, mouse genetics, phenotypic analysis of lysosome-related organelle biogenesis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — foundational positional cloning with clear organelle phenotype, highly cited","pmids":["12538872"],"is_preprint":false},{"year":2009,"finding":"Drosophila Vps33A (carnation/Car) is specifically required for late endosome-to-lysosome fusion and autophagosome-lysosome fusion; Car binds dSyntaxin16 (present on lysosomes) in vitro, whereas dVps33B preferentially binds the early endosomal Avalanche SNARE, explaining their distinct pathway specificities.","method":"Null allele generation, genetic analysis, in vitro SNARE binding assays, fluorescence microscopy of endocytic trafficking","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 — null allele plus in vitro binding distinguishing two paralogs with orthogonal methods","pmids":["19158398"],"is_preprint":false},{"year":2015,"finding":"The VPS33A D251E point mutation (buff mouse) selectively impairs autophagosome-lysosome fusion without compromising the endocytic pathway; mutant VPS33A(D251E) shows enhanced association with the autophagic SNARE complex (STX17-VAMP8-SNAP29) and enhanced interaction with HOPS subunits VPS41, VPS39, VPS18, and VPS11, but reduced interaction with VPS16; a separate VPS33A(Y440D) mutation that reduces HOPS subunit interactions also decreases STX17 association.","method":"Co-immunoprecipitation, autophagy flux assays, buff mouse in vivo analysis, site-directed mutagenesis","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 — multiple Co-IPs with structure-guided mutations plus in vivo mouse model","pmids":["26259518"],"is_preprint":false},{"year":2019,"finding":"VPS33A interacts with syntaxin 17 (Stx17) N-peptide to regulate autophagosomal SNARE assembly; in situ FLIM-FRET showed that Stx17 heterotrimerizes with SNAP29 and VAMP7 for autophagosome fusion; VPS33A provides multimodal SM-protein regulation of this SNARE complex, and a phosphoserine in the Stx17 N-peptide acts as a master-switch controlling fusion competency.","method":"FLIM-FRET in HeLa cells, in situ protein interaction mapping, mutagenesis of Stx17 N-peptide phosphosite","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — novel FLIM-FRET approach in cells, single lab, moderate orthogonal validation","pmids":["30655294"],"is_preprint":false},{"year":2009,"finding":"VPS33A is required for fusion of uroplakin-degrading multivesicular bodies (MVBs) with lysosomes in bladder urothelial cells; buff (D251E) mice accumulate MVBs and show increased lysosomal enzyme activities, indicating a block in MVB-lysosome fusion.","method":"Buff mouse analysis, electron microscopy, immunofluorescence, lysosomal enzyme activity assays","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo mouse model with defined organelle phenotype, single lab","pmids":["19566896"],"is_preprint":false},{"year":2009,"finding":"VPS33A interacts directly with the cytoplasmic tail of RANKL (identified by pull-down); knockdown of Vps33a disrupts RANKL transport from the Golgi to secretory lysosomes, causing RANKL accumulation in the Golgi and reducing lysosomal storage of RANKL, thereby affecting regulated surface expression of RANKL in osteoblastic cells.","method":"Protein pull-down, siRNA knockdown, immunofluorescence, flow cytometry","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 3 — pull-down plus functional KD assay, single lab","pmids":["19419298"],"is_preprint":false},{"year":2018,"finding":"BioID proximity biotinylation showed VPS33A co-localizes with CORVET and HOPS subunits and with class III PI3K complex components (PIK3C3, PIK3R4, NRBF2, UVRAG, RUBICON) but not with VPS33B-associated proteins; VPS33A and VPS33B have distinct sub-cellular localizations and non-overlapping interactomes.","method":"BioID proximity biotinylation, mass spectrometry, gel filtration","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 — proteome-wide proximity assay with MS, single lab","pmids":["29778605"],"is_preprint":false},{"year":2019,"finding":"The VPS33A R498W missense mutation (Yakut MPS-plus patients) destabilizes VPS33A folding (predicted by 3D crystal structure) and reduces abundance of full-length VPS33A and other HOPS/CORVET subunits via proteasomal degradation; treatment with the proteasome inhibitor bortezomib rescues mutant protein levels; the mutation causes lysosomal over-acidification and impairs endocytic trafficking of lactosylceramide.","method":"Crystal structure analysis, immunoblotting, proteasome inhibitor treatment, glycosphingolipid trafficking assay in patient fibroblasts","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 1-2 — structure-based prediction validated by biochemical rescue, single lab","pmids":["31070736"],"is_preprint":false},{"year":2017,"finding":"The VPS33A R498W mutation (MPS-plus disease) causes lysosomal over-acidification and heparan sulphate accumulation without disrupting canonical endocytic or autophagic pathways, revealing a novel role of VPS33A in lysosomal pH regulation distinct from its fusion-tethering function.","method":"Patient-derived cell analysis, lysosomal pH measurement, GAG quantification, siRNA knockdown in HeLa cells","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — patient-derived cells plus knockdown with biochemical readouts, single lab","pmids":["28013294"],"is_preprint":false},{"year":2025,"finding":"VPS33A is required for renin granule (RG) biogenesis in juxtaglomerular cells; buff (D251E) mice have smaller RGs and reduced active renin; knockdown of Vps33a, Snap23, Stx11, and Vamp8 impairs RG biogenesis in As4.1 cells; mutant VPS33A(D251E) shows enhanced interaction with Stx11, implicating the SNARE complex Snap23-Stx11-Vamp8 in VPS33A-regulated RG fusion.","method":"Mouse knockout analysis, siRNA knockdown, co-immunoprecipitation, electron microscopy","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo mouse model plus Co-IP and cell-based KD, single lab","pmids":["40855995"],"is_preprint":false},{"year":2024,"finding":"In C. elegans, a M376I mutation in domain 3a of VPS33A suppresses the temperature-sensitive lethality caused by loss of the SM protein VPS45, demonstrating that domain 3a of VPS33A is functionally important for SNARE complex assembly in endosomal trafficking.","method":"Genetic suppressor screen in C. elegans, site-specific mutation analysis","journal":"microPublication biology","confidence":"Low","confidence_rationale":"Tier 3 — genetic epistasis in C. elegans (ortholog context), single suppressor mutation, no biochemical validation","pmids":["38585203"],"is_preprint":false},{"year":2026,"finding":"VPS33A interacts with ULK1 and supports autophagic flux; VPS33A knockdown reduces ULK1 protein levels and suppresses autophagy, while ULK1 overexpression restores autophagic activity downstream of VPS33A depletion, placing VPS33A upstream of ULK1 in autophagy regulation in cholangiocarcinoma cells.","method":"siRNA knockdown, ULK1 overexpression rescue, GFP-RFP-LC3 flux assay, correlation analysis","journal":"Digestive diseases and sciences","confidence":"Low","confidence_rationale":"Tier 3 — single lab, correlation-based interaction claim, limited mechanistic detail","pmids":["41718964"],"is_preprint":false}],"current_model":"VPS33A is a Sec1/Munc18-family SM protein that is recruited to the HOPS (and CORVET) membrane-tethering complex via a direct interaction with VPS16 (residues 642-736), where it regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, and autophagosomes with lysosomes by engaging the relevant syntaxin SNAREs (including STX17 for autophagosomal fusion and dSyntaxin16 for lysosomal fusion), with its domain 3a critical for SNARE complex assembly and its activity also required for biogenesis of lysosome-related organelles such as melanosomes, platelet granules, and renin granules."},"narrative":{"teleology":[{"year":2003,"claim":"Positional cloning of the buff mouse established VPS33A as the first mammalian component of the class C VPS/tethering complex and demonstrated that its loss causes defective biogenesis of lysosomes, melanosomes, and storage granules, linking SM-protein function to lysosome-related organelle pathways in mammals.","evidence":"Positional cloning and phenotypic analysis of the buff mouse","pmids":["12538872"],"confidence":"High","gaps":["No structural information on VPS33A or its complex interfaces","Mechanism by which the D251E mutation impairs organelle biogenesis was unknown","Whether VPS33A and the paralog VPS33B have overlapping or distinct functions was unresolved"]},{"year":2009,"claim":"Genetic and biochemical studies in Drosophila and mouse distinguished VPS33A as specifically required for late endosome–lysosome and autophagosome–lysosome fusion, showing it binds lysosomal syntaxins (dSyntaxin16) while VPS33B preferentially binds early endosomal SNAREs, and confirmed its necessity for MVB–lysosome fusion in mammalian urothelial cells.","evidence":"Drosophila null alleles with in vitro SNARE binding assays; buff mouse EM and lysosomal enzyme assays in urothelial cells","pmids":["19158398","19566896"],"confidence":"High","gaps":["Structural basis of VPS33A–VPS16 and VPS33A–SNARE interactions unknown","Whether VPS33A roles in autophagy are separable from endosomal fusion roles was unclear"]},{"year":2013,"claim":"The crystal structure of human VPS33A confirmed its SM-family fold and defined the VPS16 binding interface, establishing that VPS16 residues 642–736 are necessary and sufficient for HOPS recruitment and enabling structure-guided dissection of complex assembly.","evidence":"X-ray crystallography, mutagenesis, in vitro binding assays, and cell-based rescue","pmids":["23901104"],"confidence":"High","gaps":["SNARE-binding surfaces on VPS33A not yet mapped structurally","How other HOPS subunits depend on VPS33A–VPS16 assembly was untested"]},{"year":2015,"claim":"Structure-guided mutagenesis demonstrated that disruption of the VPS33A–VPS16 interface blocks both endosome–lysosome and autophagosome–lysosome fusion, and that the buff D251E mutation selectively impairs autophagosome–lysosome fusion while paradoxically enhancing association with the autophagic SNARE complex (STX17–VAMP8–SNAP29), revealing that binding affinity and productive SNARE engagement are distinct.","evidence":"Co-immunoprecipitation, siRNA depletion, fluorescent dextran delivery, autophagy flux assays in cells and buff mice","pmids":["25783203","26259518"],"confidence":"High","gaps":["How enhanced SNARE binding leads to fusion failure was mechanistically unexplained","Whether D251E affects SNARE complex disassembly or proofreading was not tested"]},{"year":2017,"claim":"Analysis of patient-derived fibroblasts carrying the VPS33A R498W mutation revealed that VPS33A regulates lysosomal pH homeostasis, with the mutation causing lysosomal over-acidification and heparan sulphate accumulation characteristic of MPS-plus disease, a function partially separable from canonical endocytic/autophagic fusion.","evidence":"Patient fibroblast analysis, lysosomal pH measurement, GAG quantification, siRNA knockdown in HeLa cells","pmids":["28013294"],"confidence":"Medium","gaps":["Mechanism linking VPS33A to pH regulation is unknown—whether direct or via impaired ion channel trafficking","Whether this phenotype is specific to R498W or general to VPS33A loss was not distinguished"]},{"year":2018,"claim":"BioID proximity labeling showed that VPS33A resides with CORVET, HOPS, and class III PI3K complex components in a compartment distinct from VPS33B, establishing non-overlapping interactomes for the two SM-protein paralogs at a proteome-wide scale.","evidence":"BioID proximity biotinylation and mass spectrometry","pmids":["29778605"],"confidence":"Medium","gaps":["Proximity does not prove direct binding for PI3K complex components","Functional significance of VPS33A–PI3K proximity was not tested"]},{"year":2019,"claim":"Biochemical and structural analyses showed that VPS33A R498W destabilizes protein folding, leading to proteasomal degradation of VPS33A and associated HOPS/CORVET subunits, and that proteasome inhibitor treatment rescues protein levels, explaining the molecular basis of MPS-plus pathogenesis; concurrently, FLIM-FRET revealed that VPS33A engages the STX17 N-peptide to control autophagosomal SNARE trimerization, with a phosphoserine acting as a fusion-competency switch.","evidence":"Crystal structure analysis with immunoblotting and proteasome inhibitor rescue in patient fibroblasts; FLIM-FRET in HeLa cells with mutagenesis","pmids":["31070736","30655294"],"confidence":"Medium","gaps":["In vitro reconstitution of VPS33A-catalyzed SNARE assembly has not been achieved","Kinase responsible for STX17 N-peptide phosphorylation unidentified","Whether bortezomib rescue restores function in vivo remains untested"]},{"year":2024,"claim":"A suppressor screen in C. elegans identified a gain-of-function mutation in domain 3a of VPS33A that compensates for loss of the SM protein VPS45, implicating domain 3a specifically in SNARE complex assembly during endosomal trafficking.","evidence":"Genetic suppressor screen in C. elegans with site-specific mutation analysis","pmids":["38585203"],"confidence":"Low","gaps":["No biochemical validation that domain 3a directly contacts SNAREs","Cross-species relevance to mammalian VPS33A not confirmed","Single suppressor allele—specificity of the domain 3a requirement is tentative"]},{"year":2025,"claim":"VPS33A was shown to regulate renin granule biogenesis in juxtaglomerular cells via the SNAP23–STX11–VAMP8 SNARE complex, extending its organelle-specific functions to secretory granules of the renin–angiotensin system.","evidence":"Buff mouse analysis, siRNA knockdown, Co-IP, and electron microscopy in As4.1 cells","pmids":["40855995"],"confidence":"Medium","gaps":["Whether VPS33A directly catalyzes SNAP23–STX11–VAMP8 complex assembly or acts indirectly through HOPS tethering is unresolved","Physiological impact on blood pressure regulation in buff mice not characterized"]},{"year":null,"claim":"Key unresolved questions include: the structural basis of VPS33A engagement with SNARE bundles, whether its pH-regulatory role is mechanistically distinct from tethering/fusion, and how domain 3a catalyzes SNARE complex assembly at the molecular level.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of VPS33A bound to a SNARE complex","In vitro reconstitution of VPS33A-catalyzed SNARE assembly is lacking","Mechanism of lysosomal pH regulation by VPS33A is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,4,5]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,3,6,8]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[2,3,6,10]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[6,7,11]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1,4,5]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,3,6,7]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2,10,11]}],"complexes":["HOPS","CORVET"],"partners":["VPS16","STX17","VPS41","VPS39","VPS18","VPS11","VAMP8","STX11"],"other_free_text":[]},"mechanistic_narrative":"VPS33A is a Sec1/Munc18 (SM)-family protein that functions as a core subunit of the HOPS and CORVET tethering complexes to regulate SNARE-mediated membrane fusion at late endosomes, multivesicular bodies, autophagosomes, and lysosomes. VPS33A is recruited to HOPS through a direct interaction with VPS16 (residues 642–736), and structure-guided mutations at this interface abolish both complex assembly and lysosome fusion in cells [PMID:23901104, PMID:25783203]. It engages cognate syntaxin SNAREs—STX17 for autophagosome–lysosome fusion and STX11/dSyntaxin16 for lysosomal fusion—with its domain 3a critical for SNARE complex assembly, and a phosphoserine switch in the STX17 N-peptide regulates fusion competency [PMID:19158398, PMID:30655294, PMID:40855995, PMID:38585203]. Loss-of-function mutations cause defective biogenesis of lysosome-related organelles including melanosomes, platelet dense granules, and renin granules in the buff mouse, and the homozygous R498W missense mutation causes MPS-plus syndrome in humans, characterized by heparan sulphate accumulation and lysosomal over-acidification [PMID:12538872, PMID:28013294, PMID:31070736]."},"prefetch_data":{"uniprot":{"accession":"Q96AX1","full_name":"Vacuolar protein sorting-associated protein 33A","aliases":[],"length_aa":596,"mass_kda":67.6,"function":"Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS16 but not VIPAS39 (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770)","subcellular_location":"Cytoplasmic vesicle; Late endosome membrane; Lysosome membrane; Early endosome; Cytoplasmic vesicle, autophagosome; Cytoplasmic vesicle, clathrin-coated vesicle","url":"https://www.uniprot.org/uniprotkb/Q96AX1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS33A","classification":"Common Essential","n_dependent_lines":875,"n_total_lines":1208,"dependency_fraction":0.7243377483443708},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000139719","cell_line_id":"CID001859","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":3},{"compartment":"nucleoplasm","grade":1}],"interactors":[{"gene":"VPS16","stoichiometry":10.0},{"gene":"VPS18","stoichiometry":10.0},{"gene":"NRIP1","stoichiometry":0.2},{"gene":"TGFBRAP1","stoichiometry":0.2},{"gene":"VPS11","stoichiometry":0.2},{"gene":"VPS41","stoichiometry":0.2},{"gene":"VPS8","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001859","total_profiled":1310},"omim":[{"mim_id":"619389","title":"SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29","url":"https://www.omim.org/entry/619389"},{"mim_id":"617303","title":"MUCOPOLYSACCHARIDOSIS-PLUS SYNDROME; MPSPS","url":"https://www.omim.org/entry/617303"},{"mim_id":"613401","title":"VPS33B-INTERACTING PROTEIN, APICAL-BASOLATERAL POLARITY REGULATOR, SPE39 HOMOLOG; VIPAS39","url":"https://www.omim.org/entry/613401"},{"mim_id":"610034","title":"VPS33A CORE SUBUNIT OF CORVET AND HOPS COMPLEXES; VPS33A","url":"https://www.omim.org/entry/610034"},{"mim_id":"608549","title":"VPS11 CORE SUBUNIT OF CORVET AND HOPS COMPLEXES; VPS11","url":"https://www.omim.org/entry/608549"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS33A"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q96AX1","domains":[{"cath_id":"3.40.50.2060","chopping":"2-142","consensus_level":"high","plddt":94.566,"start":2,"end":142},{"cath_id":"3.40.50.1910","chopping":"143-235_471-596","consensus_level":"medium","plddt":93.5479,"start":143,"end":596},{"cath_id":"3.90.830.10","chopping":"245-271_281-366","consensus_level":"medium","plddt":94.5366,"start":245,"end":366},{"cath_id":"1.25.40.850","chopping":"368-417_419-459","consensus_level":"medium","plddt":96.901,"start":368,"end":459}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96AX1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96AX1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96AX1-F1-predicted_aligned_error_v6.png","plddt_mean":93.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS33A","jax_strain_url":"https://www.jax.org/strain/search?query=VPS33A"},"sequence":{"accession":"Q96AX1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96AX1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96AX1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96AX1"}},"corpus_meta":[{"pmid":"25783203","id":"PMC_25783203","title":"Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes.","date":"2015","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/25783203","citation_count":125,"is_preprint":false},{"pmid":"12538872","id":"PMC_12538872","title":"The mouse organellar biogenesis mutant buff results from a mutation in Vps33a, a homologue of yeast vps33 and Drosophila carnation.","date":"2003","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12538872","citation_count":107,"is_preprint":false},{"pmid":"23901104","id":"PMC_23901104","title":"Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23901104","citation_count":81,"is_preprint":false},{"pmid":"19158398","id":"PMC_19158398","title":"The SM protein Car/Vps33A regulates SNARE-mediated trafficking to lysosomes and lysosome-related organelles.","date":"2009","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/19158398","citation_count":79,"is_preprint":false},{"pmid":"28013294","id":"PMC_28013294","title":"Mutation in VPS33A affects metabolism of glycosaminoglycans: a new type of mucopolysaccharidosis with severe systemic symptoms.","date":"2017","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28013294","citation_count":55,"is_preprint":false},{"pmid":"26259518","id":"PMC_26259518","title":"Impairment of autophagosome-lysosome fusion in the buff mutant mice with the VPS33A(D251E) mutation.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26259518","citation_count":44,"is_preprint":false},{"pmid":"31070736","id":"PMC_31070736","title":"The lysosomal disease caused by mutant VPS33A.","date":"2019","source":"Human molecular 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genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40758165","citation_count":3,"is_preprint":false},{"pmid":"38585203","id":"PMC_38585203","title":"Domain 3a mutation of VPS33A suppresses larval arrest phenotype in the loss of VPS45 in Caenorhabditis elegans.","date":"2024","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/38585203","citation_count":0,"is_preprint":false},{"pmid":"40855995","id":"PMC_40855995","title":"Impaired biogenesis of renin granules in juxtaglomerular cells of Vps33a (D251E) mutant mice.","date":"2025","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/40855995","citation_count":0,"is_preprint":false},{"pmid":"41718964","id":"PMC_41718964","title":"VPS33A Promotes Pemigatinib Resistance in Cholangiocarcinoma via Autophagy.","date":"2026","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41718964","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10454,"output_tokens":3371,"usd":0.040963},"stage2":{"model":"claude-opus-4-6","input_tokens":6750,"output_tokens":2922,"usd":0.1602},"total_usd":0.201163,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structure of human VPS33A confirmed its identity as a Sec1/Munc18 (SM) family member; VPS16 residues 642-736 are necessary and sufficient to recruit VPS33A to the HOPS complex; mutations at the VPS33A-VPS16 binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.\",\n      \"method\": \"X-ray crystallography, in vitro binding assays, mutagenesis, cell-based rescue experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus mutagenesis validated in vitro and in cells\",\n      \"pmids\": [\"23901104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"VPS33A is recruited to the HOPS complex via its interaction with VPS16; VPS16/VPS33A interface mutants that abolish binding fail to rescue lysosome fusion with endosomes or autophagosomes; the entire HOPS complex (including VPS33A) is required for endosome-lysosome and autophagosome-lysosome fusion, whereas the paralogous VPS33B/VIPAR complex is not.\",\n      \"method\": \"Crystal structure-guided mutagenesis, siRNA depletion, fluorescent dextran delivery assay, immunoprecipitation\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — structure-guided mutagenesis combined with functional rescue and orthogonal trafficking assays\",\n      \"pmids\": [\"25783203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"VPS33A is a mammalian Sec1-family protein orthologous to yeast Vps33 and Drosophila carnation; loss-of-function (buff mouse point mutation) causes defective biogenesis of lysosomes, melanosomes, and storage granules, identifying VPS33A as the first mammalian component of the class C vacuole/prevacuole-associated t-SNARE complex.\",\n      \"method\": \"Positional cloning, mouse genetics, phenotypic analysis of lysosome-related organelle biogenesis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — foundational positional cloning with clear organelle phenotype, highly cited\",\n      \"pmids\": [\"12538872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Drosophila Vps33A (carnation/Car) is specifically required for late endosome-to-lysosome fusion and autophagosome-lysosome fusion; Car binds dSyntaxin16 (present on lysosomes) in vitro, whereas dVps33B preferentially binds the early endosomal Avalanche SNARE, explaining their distinct pathway specificities.\",\n      \"method\": \"Null allele generation, genetic analysis, in vitro SNARE binding assays, fluorescence microscopy of endocytic trafficking\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — null allele plus in vitro binding distinguishing two paralogs with orthogonal methods\",\n      \"pmids\": [\"19158398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The VPS33A D251E point mutation (buff mouse) selectively impairs autophagosome-lysosome fusion without compromising the endocytic pathway; mutant VPS33A(D251E) shows enhanced association with the autophagic SNARE complex (STX17-VAMP8-SNAP29) and enhanced interaction with HOPS subunits VPS41, VPS39, VPS18, and VPS11, but reduced interaction with VPS16; a separate VPS33A(Y440D) mutation that reduces HOPS subunit interactions also decreases STX17 association.\",\n      \"method\": \"Co-immunoprecipitation, autophagy flux assays, buff mouse in vivo analysis, site-directed mutagenesis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple Co-IPs with structure-guided mutations plus in vivo mouse model\",\n      \"pmids\": [\"26259518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"VPS33A interacts with syntaxin 17 (Stx17) N-peptide to regulate autophagosomal SNARE assembly; in situ FLIM-FRET showed that Stx17 heterotrimerizes with SNAP29 and VAMP7 for autophagosome fusion; VPS33A provides multimodal SM-protein regulation of this SNARE complex, and a phosphoserine in the Stx17 N-peptide acts as a master-switch controlling fusion competency.\",\n      \"method\": \"FLIM-FRET in HeLa cells, in situ protein interaction mapping, mutagenesis of Stx17 N-peptide phosphosite\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — novel FLIM-FRET approach in cells, single lab, moderate orthogonal validation\",\n      \"pmids\": [\"30655294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"VPS33A is required for fusion of uroplakin-degrading multivesicular bodies (MVBs) with lysosomes in bladder urothelial cells; buff (D251E) mice accumulate MVBs and show increased lysosomal enzyme activities, indicating a block in MVB-lysosome fusion.\",\n      \"method\": \"Buff mouse analysis, electron microscopy, immunofluorescence, lysosomal enzyme activity assays\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo mouse model with defined organelle phenotype, single lab\",\n      \"pmids\": [\"19566896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"VPS33A interacts directly with the cytoplasmic tail of RANKL (identified by pull-down); knockdown of Vps33a disrupts RANKL transport from the Golgi to secretory lysosomes, causing RANKL accumulation in the Golgi and reducing lysosomal storage of RANKL, thereby affecting regulated surface expression of RANKL in osteoblastic cells.\",\n      \"method\": \"Protein pull-down, siRNA knockdown, immunofluorescence, flow cytometry\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — pull-down plus functional KD assay, single lab\",\n      \"pmids\": [\"19419298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"BioID proximity biotinylation showed VPS33A co-localizes with CORVET and HOPS subunits and with class III PI3K complex components (PIK3C3, PIK3R4, NRBF2, UVRAG, RUBICON) but not with VPS33B-associated proteins; VPS33A and VPS33B have distinct sub-cellular localizations and non-overlapping interactomes.\",\n      \"method\": \"BioID proximity biotinylation, mass spectrometry, gel filtration\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — proteome-wide proximity assay with MS, single lab\",\n      \"pmids\": [\"29778605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The VPS33A R498W missense mutation (Yakut MPS-plus patients) destabilizes VPS33A folding (predicted by 3D crystal structure) and reduces abundance of full-length VPS33A and other HOPS/CORVET subunits via proteasomal degradation; treatment with the proteasome inhibitor bortezomib rescues mutant protein levels; the mutation causes lysosomal over-acidification and impairs endocytic trafficking of lactosylceramide.\",\n      \"method\": \"Crystal structure analysis, immunoblotting, proteasome inhibitor treatment, glycosphingolipid trafficking assay in patient fibroblasts\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 — structure-based prediction validated by biochemical rescue, single lab\",\n      \"pmids\": [\"31070736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The VPS33A R498W mutation (MPS-plus disease) causes lysosomal over-acidification and heparan sulphate accumulation without disrupting canonical endocytic or autophagic pathways, revealing a novel role of VPS33A in lysosomal pH regulation distinct from its fusion-tethering function.\",\n      \"method\": \"Patient-derived cell analysis, lysosomal pH measurement, GAG quantification, siRNA knockdown in HeLa cells\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — patient-derived cells plus knockdown with biochemical readouts, single lab\",\n      \"pmids\": [\"28013294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VPS33A is required for renin granule (RG) biogenesis in juxtaglomerular cells; buff (D251E) mice have smaller RGs and reduced active renin; knockdown of Vps33a, Snap23, Stx11, and Vamp8 impairs RG biogenesis in As4.1 cells; mutant VPS33A(D251E) shows enhanced interaction with Stx11, implicating the SNARE complex Snap23-Stx11-Vamp8 in VPS33A-regulated RG fusion.\",\n      \"method\": \"Mouse knockout analysis, siRNA knockdown, co-immunoprecipitation, electron microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo mouse model plus Co-IP and cell-based KD, single lab\",\n      \"pmids\": [\"40855995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In C. elegans, a M376I mutation in domain 3a of VPS33A suppresses the temperature-sensitive lethality caused by loss of the SM protein VPS45, demonstrating that domain 3a of VPS33A is functionally important for SNARE complex assembly in endosomal trafficking.\",\n      \"method\": \"Genetic suppressor screen in C. elegans, site-specific mutation analysis\",\n      \"journal\": \"microPublication biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — genetic epistasis in C. elegans (ortholog context), single suppressor mutation, no biochemical validation\",\n      \"pmids\": [\"38585203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"VPS33A interacts with ULK1 and supports autophagic flux; VPS33A knockdown reduces ULK1 protein levels and suppresses autophagy, while ULK1 overexpression restores autophagic activity downstream of VPS33A depletion, placing VPS33A upstream of ULK1 in autophagy regulation in cholangiocarcinoma cells.\",\n      \"method\": \"siRNA knockdown, ULK1 overexpression rescue, GFP-RFP-LC3 flux assay, correlation analysis\",\n      \"journal\": \"Digestive diseases and sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, correlation-based interaction claim, limited mechanistic detail\",\n      \"pmids\": [\"41718964\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS33A is a Sec1/Munc18-family SM protein that is recruited to the HOPS (and CORVET) membrane-tethering complex via a direct interaction with VPS16 (residues 642-736), where it regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, and autophagosomes with lysosomes by engaging the relevant syntaxin SNAREs (including STX17 for autophagosomal fusion and dSyntaxin16 for lysosomal fusion), with its domain 3a critical for SNARE complex assembly and its activity also required for biogenesis of lysosome-related organelles such as melanosomes, platelet granules, and renin granules.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"VPS33A is a Sec1/Munc18 (SM)-family protein that functions as a core subunit of the HOPS and CORVET tethering complexes to regulate SNARE-mediated membrane fusion at late endosomes, multivesicular bodies, autophagosomes, and lysosomes. VPS33A is recruited to HOPS through a direct interaction with VPS16 (residues 642–736), and structure-guided mutations at this interface abolish both complex assembly and lysosome fusion in cells [PMID:23901104, PMID:25783203]. It engages cognate syntaxin SNAREs—STX17 for autophagosome–lysosome fusion and STX11/dSyntaxin16 for lysosomal fusion—with its domain 3a critical for SNARE complex assembly, and a phosphoserine switch in the STX17 N-peptide regulates fusion competency [PMID:19158398, PMID:30655294, PMID:40855995, PMID:38585203]. Loss-of-function mutations cause defective biogenesis of lysosome-related organelles including melanosomes, platelet dense granules, and renin granules in the buff mouse, and the homozygous R498W missense mutation causes MPS-plus syndrome in humans, characterized by heparan sulphate accumulation and lysosomal over-acidification [PMID:12538872, PMID:28013294, PMID:31070736].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Positional cloning of the buff mouse established VPS33A as the first mammalian component of the class C VPS/tethering complex and demonstrated that its loss causes defective biogenesis of lysosomes, melanosomes, and storage granules, linking SM-protein function to lysosome-related organelle pathways in mammals.\",\n      \"evidence\": \"Positional cloning and phenotypic analysis of the buff mouse\",\n      \"pmids\": [\"12538872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural information on VPS33A or its complex interfaces\",\n        \"Mechanism by which the D251E mutation impairs organelle biogenesis was unknown\",\n        \"Whether VPS33A and the paralog VPS33B have overlapping or distinct functions was unresolved\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Genetic and biochemical studies in Drosophila and mouse distinguished VPS33A as specifically required for late endosome–lysosome and autophagosome–lysosome fusion, showing it binds lysosomal syntaxins (dSyntaxin16) while VPS33B preferentially binds early endosomal SNAREs, and confirmed its necessity for MVB–lysosome fusion in mammalian urothelial cells.\",\n      \"evidence\": \"Drosophila null alleles with in vitro SNARE binding assays; buff mouse EM and lysosomal enzyme assays in urothelial cells\",\n      \"pmids\": [\"19158398\", \"19566896\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of VPS33A–VPS16 and VPS33A–SNARE interactions unknown\",\n        \"Whether VPS33A roles in autophagy are separable from endosomal fusion roles was unclear\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The crystal structure of human VPS33A confirmed its SM-family fold and defined the VPS16 binding interface, establishing that VPS16 residues 642–736 are necessary and sufficient for HOPS recruitment and enabling structure-guided dissection of complex assembly.\",\n      \"evidence\": \"X-ray crystallography, mutagenesis, in vitro binding assays, and cell-based rescue\",\n      \"pmids\": [\"23901104\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"SNARE-binding surfaces on VPS33A not yet mapped structurally\",\n        \"How other HOPS subunits depend on VPS33A–VPS16 assembly was untested\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Structure-guided mutagenesis demonstrated that disruption of the VPS33A–VPS16 interface blocks both endosome–lysosome and autophagosome–lysosome fusion, and that the buff D251E mutation selectively impairs autophagosome–lysosome fusion while paradoxically enhancing association with the autophagic SNARE complex (STX17–VAMP8–SNAP29), revealing that binding affinity and productive SNARE engagement are distinct.\",\n      \"evidence\": \"Co-immunoprecipitation, siRNA depletion, fluorescent dextran delivery, autophagy flux assays in cells and buff mice\",\n      \"pmids\": [\"25783203\", \"26259518\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How enhanced SNARE binding leads to fusion failure was mechanistically unexplained\",\n        \"Whether D251E affects SNARE complex disassembly or proofreading was not tested\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Analysis of patient-derived fibroblasts carrying the VPS33A R498W mutation revealed that VPS33A regulates lysosomal pH homeostasis, with the mutation causing lysosomal over-acidification and heparan sulphate accumulation characteristic of MPS-plus disease, a function partially separable from canonical endocytic/autophagic fusion.\",\n      \"evidence\": \"Patient fibroblast analysis, lysosomal pH measurement, GAG quantification, siRNA knockdown in HeLa cells\",\n      \"pmids\": [\"28013294\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism linking VPS33A to pH regulation is unknown—whether direct or via impaired ion channel trafficking\",\n        \"Whether this phenotype is specific to R498W or general to VPS33A loss was not distinguished\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"BioID proximity labeling showed that VPS33A resides with CORVET, HOPS, and class III PI3K complex components in a compartment distinct from VPS33B, establishing non-overlapping interactomes for the two SM-protein paralogs at a proteome-wide scale.\",\n      \"evidence\": \"BioID proximity biotinylation and mass spectrometry\",\n      \"pmids\": [\"29778605\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Proximity does not prove direct binding for PI3K complex components\",\n        \"Functional significance of VPS33A–PI3K proximity was not tested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Biochemical and structural analyses showed that VPS33A R498W destabilizes protein folding, leading to proteasomal degradation of VPS33A and associated HOPS/CORVET subunits, and that proteasome inhibitor treatment rescues protein levels, explaining the molecular basis of MPS-plus pathogenesis; concurrently, FLIM-FRET revealed that VPS33A engages the STX17 N-peptide to control autophagosomal SNARE trimerization, with a phosphoserine acting as a fusion-competency switch.\",\n      \"evidence\": \"Crystal structure analysis with immunoblotting and proteasome inhibitor rescue in patient fibroblasts; FLIM-FRET in HeLa cells with mutagenesis\",\n      \"pmids\": [\"31070736\", \"30655294\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"In vitro reconstitution of VPS33A-catalyzed SNARE assembly has not been achieved\",\n        \"Kinase responsible for STX17 N-peptide phosphorylation unidentified\",\n        \"Whether bortezomib rescue restores function in vivo remains untested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A suppressor screen in C. elegans identified a gain-of-function mutation in domain 3a of VPS33A that compensates for loss of the SM protein VPS45, implicating domain 3a specifically in SNARE complex assembly during endosomal trafficking.\",\n      \"evidence\": \"Genetic suppressor screen in C. elegans with site-specific mutation analysis\",\n      \"pmids\": [\"38585203\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No biochemical validation that domain 3a directly contacts SNAREs\",\n        \"Cross-species relevance to mammalian VPS33A not confirmed\",\n        \"Single suppressor allele—specificity of the domain 3a requirement is tentative\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"VPS33A was shown to regulate renin granule biogenesis in juxtaglomerular cells via the SNAP23–STX11–VAMP8 SNARE complex, extending its organelle-specific functions to secretory granules of the renin–angiotensin system.\",\n      \"evidence\": \"Buff mouse analysis, siRNA knockdown, Co-IP, and electron microscopy in As4.1 cells\",\n      \"pmids\": [\"40855995\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether VPS33A directly catalyzes SNAP23–STX11–VAMP8 complex assembly or acts indirectly through HOPS tethering is unresolved\",\n        \"Physiological impact on blood pressure regulation in buff mice not characterized\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the structural basis of VPS33A engagement with SNARE bundles, whether its pH-regulatory role is mechanistically distinct from tethering/fusion, and how domain 3a catalyzes SNARE complex assembly at the molecular level.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of VPS33A bound to a SNARE complex\",\n        \"In vitro reconstitution of VPS33A-catalyzed SNARE assembly is lacking\",\n        \"Mechanism of lysosomal pH regulation by VPS33A is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 3, 6, 8]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [2, 3, 6, 10]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [6, 7, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1, 4, 5]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 3, 6, 7]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2, 10, 11]}\n    ],\n    \"complexes\": [\n      \"HOPS\",\n      \"CORVET\"\n    ],\n    \"partners\": [\n      \"VPS16\",\n      \"STX17\",\n      \"VPS41\",\n      \"VPS39\",\n      \"VPS18\",\n      \"VPS11\",\n      \"VAMP8\",\n      \"STX11\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}