{"gene":"CCZ1","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2010,"finding":"The dimeric Mon1-Ccz1 complex is the guanine nucleotide exchange factor (GEF) for the late endosomal Rab7 homolog Ypt7. The complex, but neither protein alone, counteracts GAP function in vivo, rescues in vitro fusion of vacuoles carrying Ypt7-GDP, and promotes nucleotide exchange on Ypt7 independently of Vps39/HOPS.","method":"In vitro nucleotide exchange assay, in vitro vacuole fusion assay, in vivo GAP suppression assay","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of GEF activity, multiple orthogonal assays, widely replicated across subsequent studies","pmids":["20797862"],"is_preprint":false},{"year":2002,"finding":"Mon1 and Ccz1 physically interact as a stable protein complex (the Ccz1-Mon1 complex), function in nearly all membrane-trafficking pathways targeting the vacuole, and act after transport vesicle formation but before or at the fusion step with the vacuole. The complex peripherally associates with a perivacuolar compartment.","method":"Co-immunoprecipitation, subcellular fractionation, fluorescence microscopy, genetic deletion analysis with multiple pathway readouts (Cvt, autophagy, pexophagy, CPY/ALP/MVB pathways)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, fractionation, multiple orthogonal pathway assays, replicated in subsequent work","pmids":["12364329"],"is_preprint":false},{"year":2003,"finding":"The Ccz1-Mon1 complex is required for the tethering/docking stage of homotypic vacuole fusion. In its absence, SNARE pairing integrity and the class C Vps/HOPS complex interaction with unpaired SNAREs are both impaired. The complex co-localizes with other fusion components on the vacuole as part of the cis-SNARE complex, and its vacuolar association is regulated by the class C Vps/HOPS complex.","method":"In vitro homotypic vacuole fusion assay, SNARE co-immunoprecipitation, fluorescence co-localization, genetic analysis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reconstituted in vitro fusion assay, biochemical SNARE interaction studies, multiple orthogonal methods","pmids":["14662743"],"is_preprint":false},{"year":2001,"finding":"Ccz1 physically interacts with the Rab GTPase Ypt7. Extragenic suppressors of CCZ1 deletion all mapped to mutated alleles of YPT7 (with mutations in the guanine-binding domains), and direct physical interaction was confirmed by co-immunoprecipitation.","method":"Suppressor genetics, co-immunoprecipitation","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus co-IP, single lab, two orthogonal methods","pmids":["11590240"],"is_preprint":false},{"year":2014,"finding":"Mon1-Ccz1 is recruited to endosomes and vacuoles through binding to phosphatidylinositol 3-phosphate (PI3P). After activating Ypt7, Mon1 is phosphorylated by the type 1 casein kinase Yck3 and released from vacuoles for recycling. Phosphorylation-site mutants of Mon1 are retained on vacuoles, and this retention is rescued by addition of recombinant Yck3.","method":"Lipid competition assay (PI3P), recombinant kinase add-back assay, phosphomutant analysis, vacuole membrane binding assay","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro lipid binding, recombinant kinase reconstitution, mutagenesis; multiple orthogonal methods in single lab","pmids":["24623720"],"is_preprint":false},{"year":2018,"finding":"Mon1-Ccz1 is specifically recruited to the pre-autophagosomal structure under starvation by directly binding Atg8 (yeast LC3 homolog) via at least one LIR motif in the Ccz1 C-terminus. This LIR motif is essential for autophagy but not for endosomal transport. Only wild-type, not LIR-mutated Mon1-Ccz1, promotes Atg8-dependent activation of Ypt7.","method":"LIR motif mutagenesis, in vitro binding assay, GEF activity assay, fluorescence microscopy, yeast genetics","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — mutagenesis, in vitro binding and GEF assays, multiple orthogonal methods in single study","pmids":["29446751"],"is_preprint":false},{"year":2016,"finding":"The Ccz1-Mon1-Rab7 module is required for autophagosome-lysosome fusion in Drosophila fat cells. Rab5 is dispensable for the Ccz1-Mon1-dependent recruitment of Rab7 to PI3P-positive autophagosomes (which are generated by Atg14-containing Vps34 PI3 kinase complex), placing the Ccz1-Mon1 complex downstream of PI3P generation and upstream of autophagosome-lysosome fusion.","method":"Genetic loss-of-function (Drosophila mutants), fluorescence microscopy, autophagosome quantification, epistasis analysis","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with defined phenotypic readout, multiple mutant combinations tested, single lab","pmids":["27559127"],"is_preprint":false},{"year":2015,"finding":"Mon1-Ccz1 activates Rab7 specifically on late endosomes in mammalian cells; Rab7 activity on lysosomes is independent of Mon1-Ccz1. Mon1-Ccz1 dissociates from lysosomes after late endosome-lysosome fusion. Active Rab7 on lysosomes (independent of Mon1-Ccz1) plays a role in perinuclear lysosome clustering.","method":"FRET-based Rab7 activity sensor, confocal FRET imaging, siRNA knockdown of Mon1-Ccz1, EGF-induced macropinocytosis assay","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — FRET biosensor with knockdown, single lab, two orthogonal approaches","pmids":["26627821"],"is_preprint":false},{"year":2017,"finding":"C18orf8/RMC1 is a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor complex and positively regulates RAB7 recruitment to late endosomes/autophagosomes. This was identified through interaction proteomics of proteins accumulating in GABARAP/L1/L2-deficient cells.","method":"Interaction proteomics (AP-MS), genetic cell engineering (ATG8 knockouts), quantitative autophagosome proteomics","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — AP-MS identification with functional validation in KO cells, single lab","pmids":["29038162"],"is_preprint":false},{"year":2021,"finding":"C5orf51 is a component of the MON1-CCZ1 complex, identified as an interactor of GDP-locked RAB7A by proximity biotinylation. In the absence of C5orf51, RAB7A localization on depolarized mitochondria is compromised and RAB7A is degraded by the proteasome, indicating C5orf51 stabilizes RAB7A and supports its mitochondrial recruitment during mitophagy.","method":"Proximity-dependent biotinylation (miniTurbo), co-immunoprecipitation, knockout cell analysis, fluorescence microscopy","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity biotinylation plus Co-IP plus KO phenotype, single lab, multiple orthogonal methods","pmids":["34432599"],"is_preprint":false},{"year":2022,"finding":"The lysosomal V-ATPase a3 subunit interacts with the Mon1A-Ccz1 complex (GEF for Rab7) via the amino-terminal half domain of a3 and the longin motifs of Mon1A and Ccz1. This interaction is required for Mon1A-Ccz1 localization to secretory lysosomes in osteoclasts, which mediates Rab7 recruitment to the organelle.","method":"Co-immunoprecipitation in HEK293T cells, domain mapping by truncation mutants, endogenous Ccz1 localization analysis in a3-knockout osteoclasts","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping plus KO localization phenotype, single lab","pmids":["35589873"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM structure of the metazoan Mon1-Ccz1-Bulli (MCBulli) complex was solved at 3.2 Å resolution. Bulli associates as a leg-like extension at the periphery of the Mon1-Ccz1 heterodimer and does not impact GEF activity or interactions with recruiter/substrate GTPases, but likely serves as a recruitment platform for additional regulators of endolysosomal trafficking.","method":"Cryo-electron microscopy (3.2 Å), structural analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution cryo-EM structure with functional interpretation; single study but rigorous structural method","pmids":["37155863"],"is_preprint":false},{"year":2023,"finding":"An amphipathic helix in Ccz1 is required for Mon1-Ccz1 function in autophagy but not endosomal maturation, revealing a mechanism for differential targeting to autophagosomes vs. endosomes. The Ccz1 amphipathic helix interacts with lipid packing defects, Mon1 basic patches bind positively charged lipids, and association with recruiter proteins synergistically governs membrane recruitment. Interaction with recruiter proteins can further stimulate GEF activity beyond membrane concentration effects.","method":"Mutagenesis, lipid-binding assays, in vitro GEF activity assays, yeast functional genetics","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — mutagenesis, in vitro lipid and GEF assays, multiple orthogonal methods in single study","pmids":["36649906"],"is_preprint":false},{"year":2023,"finding":"CCZ1 controls early-to-late endosomal trafficking of Marburg and Ebola filoviruses, functioning as an essential host factor in the early stage of filovirus replication. Loss of CCZ1 nearly completely abolishes Marburg and Ebola infections, validated in 3D primary human hepatocyte cultures and blood-vessel organoids.","method":"Haploid cell genetic screen, CCZ1 knockout validation, 3D primary human tissue models (hepatocyte cultures, blood-vessel organoids), viral infection assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic screen plus KO validation in multiple cell/tissue models, single study","pmids":["37880247"],"is_preprint":false},{"year":2022,"finding":"CCZ1-MON1A complex dysfunction causes decreased active RAB7 on autophagosome fractions in Alzheimer's disease models. Overexpressing CCZ1-MON1A increases active RAB7, enhances autophagosome maturation, and promotes degradation of APP-CTFs, Aβ, and P-tau in an autophagy-dependent manner.","method":"Autophagosome fractionation, GST-R7BD affinity isolation assay for GTP-RAB7, AAV-mediated overexpression in mouse brain, immunoblotting","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical GEF activity assay on isolated autophagosomes, in vivo AAV overexpression, multiple readouts; single lab","pmids":["35198070"],"is_preprint":false},{"year":2025,"finding":"Structural and biochemical comparison of Mon1-Ccz1 and Fuzzy-Inturned reveals that both tri-longin domain GEF complexes use a conserved sequence motif of their substrate GTPases for catalysis, while secondary interactions mediate target discrimination. The metazoan RMC1/Bulli subunit mediates membrane recruitment of the Mon1-Ccz1 GEF complex via electrostatic interactions through a distinct interface from the fungal dimer, demonstrated by protein-lipid interaction studies and functional characterization in flies.","method":"Structural determination, protein-lipid interaction assays, in vitro reconstitution, functional genetics in Drosophila","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Moderate — structural analysis combined with in vitro reconstitution, lipid interaction assays, and in vivo functional genetics; multiple orthogonal methods","pmids":["40864718"],"is_preprint":false},{"year":2010,"finding":"In C. elegans, CCZ-1 mediates digestion of apoptotic corpses by acting in phagosome maturation through recruitment of the GTPase RAB-7 to phagosomes, placing CCZ-1 upstream of RAB-7 in the phagosome maturation pathway.","method":"Genetic loss-of-function (C. elegans deletion mutants), fluorescence microscopy of corpse persistence and RAB-7 recruitment","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotype and RAB-7 localization readout, single lab","pmids":["20519582"],"is_preprint":false},{"year":2014,"finding":"In C. elegans, CCZ-1 functions independently of SAND-1 (Mon1 ortholog) in gut granule (lysosome-related organelle) biogenesis, possibly acting with GLO-3 as a GEF for the Rab32/38-related GTPase GLO-1. Point mutations in GLO-1 predicted to increase spontaneous nucleotide exchange suppress loss of gut granules by ccz-1 mutants, genetically placing CCZ-1 upstream of GLO-1.","method":"Genetic epistasis (suppressor analysis), fluorescence microscopy, C. elegans mutant analysis","journal":"Molecular biology of the cell","confidence":"Low","confidence_rationale":"Tier 3 / Weak — genetic suppressor screen suggesting CCZ-1/GLO-3 as GLO-1 GEF, but GEF activity not directly demonstrated in vitro; single lab","pmids":["24501423"],"is_preprint":false},{"year":2026,"finding":"The trimeric Bulli-Mon1-Ccz1 Rab7 GEF complex (BuMC1-GEF) interacts with Rab5, which stimulates its GEF activity during endosomal maturation in Drosophila nephrocytes. GAPsec is identified as a GAP for Rab5 required for endosomal maturation; its inactivation results in enlarged dysfunctional endosomes unable to fuse with lysosomes.","method":"Drosophila genetic loss-of-function, fluorescence microscopy of endosomal trafficking, biochemical interaction analysis","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Drosophila genetics with defined trafficking phenotype and biochemical GEF-stimulation data; single study","pmids":["41943871"],"is_preprint":false}],"current_model":"CCZ1 forms an obligate heterodimer with MON1 (and, in metazoans, a trimeric complex additionally containing RMC1/Bulli) that functions as the guanine nucleotide exchange factor (GEF) for Rab7/Ypt7, activating it specifically on late endosomes and autophagosomes to drive endosomal maturation and autophagosome-lysosome fusion; the complex is recruited to membranes through a synergistic code of PI3P binding, interaction with Atg8/LC3 (via a Ccz1 LIR motif, for autophagy-specific targeting), and electrostatic lipid interactions via a Ccz1 amphipathic helix, and its membrane association is dynamically regulated by phosphorylation of Mon1 by the casein kinase Yck3, which promotes release and recycling after Rab7 activation."},"narrative":{"mechanistic_narrative":"CCZ1 is an obligate subunit of a membrane-trafficking guanine nucleotide exchange factor (GEF) that drives endosomal maturation and autophagosome-lysosome fusion by activating the late-endosomal Rab7/Ypt7 GTPase [PMID:20797862, PMID:12364329]. CCZ1 forms a stable heterodimer with MON1, and only the assembled complex—not either protein alone—catalyzes nucleotide exchange on Ypt7, counteracts GAP activity, and rescues vacuole fusion [PMID:20797862]; CCZ1 itself contacts the substrate GTPase Ypt7 directly [PMID:11590240]. The complex acts at the tethering/docking stage of homotypic fusion, where its membrane association is governed by the HOPS/class C Vps machinery [PMID:14662743]. Membrane recruitment follows a synergistic code: binding to PI3P [PMID:24623720], an autophagy-specific LIR motif in the CCZ1 C-terminus that engages Atg8/LC3 to target pre-autophagosomal structures [PMID:29446751], and a CCZ1 amphipathic helix that reads lipid-packing defects and selectively supports autophagy over endosomal maturation [PMID:36649906]. After activating Rab7, MON1 is phosphorylated by the casein kinase Yck3, releasing the complex from the membrane for recycling [PMID:24623720]. In metazoans the complex acquires a third subunit, RMC1/Bulli, which forms a peripheral leg-like extension serving as a recruitment platform and contributing electrostatic membrane binding without altering core GEF catalysis [PMID:29038162, PMID:37155863, PMID:40864718]. The complex functions across endosomal maturation, autophagy, mitophagy, and phagosome maturation [PMID:27559127, PMID:26627821, PMID:34432599, PMID:20519582], and CCZ1 is an essential host factor for early-to-late endosomal trafficking of Ebola and Marburg filoviruses [PMID:37880247]. Restoring CCZ1-MON1A activity enhances Rab7-dependent autophagosome maturation and clearance of APP-CTFs, Aβ, and P-tau in Alzheimer's disease models [PMID:35198070].","teleology":[{"year":2001,"claim":"Establishing that CCZ1 physically engages the Rab GTPase Ypt7 connected the previously orphan CCZ1 to Rab7-dependent membrane fusion.","evidence":"suppressor genetics mapping CCZ1-deletion suppressors to YPT7 alleles, plus co-immunoprecipitation in yeast","pmids":["11590240"],"confidence":"Medium","gaps":["Did not establish whether CCZ1 acts catalytically on Ypt7 or merely binds it","Role of a CCZ1 partner not yet defined"]},{"year":2002,"claim":"Defining MON1 and CCZ1 as a stable complex acting after vesicle formation but before vacuolar fusion placed the complex at a discrete trafficking step across multiple pathways.","evidence":"reciprocal Co-IP, subcellular fractionation, and deletion analysis across Cvt, autophagy, pexophagy and MVB/CPY/ALP pathways in yeast","pmids":["12364329"],"confidence":"High","gaps":["Molecular activity of the complex not yet identified","Mechanism of perivacuolar recruitment unknown"]},{"year":2003,"claim":"Localizing CCZ1-MON1 function to the tethering/docking stage of homotypic fusion tied the complex to SNARE pairing and HOPS-regulated membrane association.","evidence":"in vitro homotypic vacuole fusion assay, SNARE Co-IP, and co-localization in yeast","pmids":["14662743"],"confidence":"High","gaps":["Did not yet define the biochemical activity (GEF) underlying the fusion defect","Causal order between HOPS and CCZ1-MON1 incompletely resolved"]},{"year":2010,"claim":"Reconstituting GEF activity demonstrated that the MON1-CCZ1 dimer—not either protein alone—is the nucleotide exchange factor for Ypt7/Rab7, defining the complex's core biochemical function.","evidence":"in vitro nucleotide exchange assay, in vitro vacuole fusion rescue, and in vivo GAP suppression; parallel C. elegans phagosome maturation genetics","pmids":["20797862","20519582"],"confidence":"High","gaps":["Did not address how the complex is targeted to specific membranes","Did not resolve autophagy- versus endosome-specific functions"]},{"year":2014,"claim":"Identifying PI3P binding and Yck3-dependent phosphorylation revealed how the GEF is recruited to and subsequently released from membranes, defining a recruitment-recycling cycle.","evidence":"PI3P lipid competition, recombinant Yck3 add-back, and phosphomutant membrane-binding assays in yeast","pmids":["24623720"],"confidence":"High","gaps":["Did not explain how recruitment is made autophagy-specific","Phospho-regulation tested in yeast only"]},{"year":2015,"claim":"FRET sensing in mammalian cells showed MON1-CCZ1 activates Rab7 specifically on late endosomes, with lysosomal Rab7 activity controlled by a distinct, complex-independent mechanism, refining the spatial logic of Rab7 activation.","evidence":"FRET-based Rab7 biosensor with siRNA knockdown and EGF-induced macropinocytosis in mammalian cells","pmids":["26627821"],"confidence":"Medium","gaps":["The MON1-CCZ1-independent lysosomal Rab7 activator not identified","Single biosensor approach in one lab"]},{"year":2016,"claim":"Drosophila genetics positioned the CCZ1-MON1-Rab7 module downstream of PI3P generation and upstream of autophagosome-lysosome fusion, independent of Rab5.","evidence":"loss-of-function mutants, autophagosome quantification, and epistasis in fly fat cells","pmids":["27559127"],"confidence":"Medium","gaps":["Did not define the molecular recruiter linking PI3P-positive autophagosomes to the complex"]},{"year":2017,"claim":"Discovery of RMC1/C18orf8 as a metazoan-specific subunit expanded the dimeric GEF into a trimeric complex that promotes Rab7 recruitment.","evidence":"interaction proteomics from GABARAP/L1/L2-deficient cells and functional validation in ATG8 knockouts","pmids":["29038162"],"confidence":"Medium","gaps":["Structural placement and catalytic contribution of RMC1 not yet defined"]},{"year":2018,"claim":"Defining a CCZ1 LIR motif that binds Atg8 explained how the complex is targeted specifically to pre-autophagosomal structures, separating autophagic from endosomal recruitment.","evidence":"LIR mutagenesis, in vitro binding and GEF assays, and microscopy in yeast","pmids":["29446751"],"confidence":"High","gaps":["Whether LIR-mediated targeting operates identically in metazoans not established"]},{"year":2021,"claim":"Identifying C5orf51 as a complex component linked MON1-CCZ1 to RAB7A stabilization and mitochondrial recruitment during mitophagy.","evidence":"miniTurbo proximity biotinylation with GDP-locked RAB7A, Co-IP, and knockout phenotyping in mammalian cells","pmids":["34432599"],"confidence":"Medium","gaps":["Relationship between C5orf51 and RMC1 within the complex unclear","Single lab"]},{"year":2022,"claim":"Mapping the V-ATPase a3 interaction and demonstrating CCZ1-MON1A's role in Alzheimer's models connected the GEF to organelle-specific recruitment and to neurodegenerative proteostasis.","evidence":"Co-IP with domain mapping in HEK293T and a3-knockout osteoclasts; autophagosome fractionation and AAV overexpression in mouse brain","pmids":["35589873","35198070"],"confidence":"Medium","gaps":["Direct GEF deficit in disease vs. compensatory effect not fully separated","Longin-domain/a3 interaction tested in limited cell types"]},{"year":2023,"claim":"Cryo-EM of the trimeric MCBulli complex and dissection of the CCZ1 amphipathic helix resolved the architecture and the dual lipid-/recruiter-based membrane code that distinguishes autophagic from endosomal targeting.","evidence":"3.2 Å cryo-EM, lipid-binding and in vitro GEF assays with mutagenesis, plus a haploid screen identifying CCZ1 as an essential filovirus host factor","pmids":["37155863","36649906","37880247"],"confidence":"High","gaps":["Regulators recruited via the Bulli leg not identified","How amphipathic helix and PI3P binding are coordinated in vivo unresolved"]},{"year":2025,"claim":"Comparative structural and biochemical analysis showed tri-longin GEFs share a conserved substrate-recognition motif while secondary interactions confer target specificity, and that metazoan RMC1/Bulli supplies electrostatic membrane recruitment through a distinct interface.","evidence":"structural determination, protein-lipid interaction assays, in vitro reconstitution, and Drosophila functional genetics","pmids":["40864718"],"confidence":"High","gaps":["Full set of secondary interactions governing in vivo specificity not enumerated"]},{"year":2026,"claim":"Demonstrating that Rab5 directly stimulates the trimeric Rab7 GEF positioned the complex within a Rab5-to-Rab7 conversion switch during endosomal maturation.","evidence":"Drosophila nephrocyte genetics, trafficking microscopy, and biochemical GEF-stimulation analysis","pmids":["41943871"],"confidence":"Medium","gaps":["Mechanistic basis of Rab5-mediated GEF stimulation not structurally defined","Single study"]},{"year":null,"claim":"How the distinct recruitment modules (PI3P, Atg8/LIR, amphipathic helix, RMC1/Bulli electrostatics, V-ATPase a3, Rab5) are integrated to select among endosomal, autophagic, mitophagic, and phagosomal targets in a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified in vivo model of compartment-selective recruitment","Regulators docking on the Bulli platform unidentified","Mammalian counterpart of Yck3 phospho-recycling not characterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,5,12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,15]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4,12,15]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[7,16]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[7,10]},{"term_id":"GO:0005773","term_label":"vacuole","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5,6,9,14]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,2,7]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,7]}],"complexes":["MON1-CCZ1 GEF complex","MON1-CCZ1-RMC1/Bulli (MCBulli) trimeric complex"],"partners":["MON1","RMC1","YPT7","RAB7A","C5ORF51","ATG8","TCIRG1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P86791","full_name":"Vacuolar fusion protein CCZ1 homolog","aliases":[],"length_aa":482,"mass_kda":55.9,"function":"Acts in concert with MON1A, as a guanine exchange factor (GEF) for RAB7, promotes the exchange of GDP to GTP, converting it from an inactive GDP-bound form into an active GTP-bound form (PubMed:23084991)","subcellular_location":"Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/P86791/entry"},"depmap":{"release":"DepMap","has_data":false,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCZ1"},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CCZ1","total_profiled":1310},"omim":[{"mim_id":"620660","title":"CCZ1 HOMOLOG, VACUOLAR PROTEIN TRAFFICKING- AND BIOGENESIS-ASSOCIATED PROTEIN; CCZ1","url":"https://www.omim.org/entry/620660"},{"mim_id":"620267","title":"REGULATOR OF MON1-CCZ1; RMC1","url":"https://www.omim.org/entry/620267"},{"mim_id":"620266","title":"RAB7A-INTERACTING MON1-CCZ1 COMPLEX SUBUNIT 1; RIMOC1","url":"https://www.omim.org/entry/620266"},{"mim_id":"611464","title":"MON1 HOMOLOG A, SECRETORY TRAFFICKING-ASSOCIATED; MON1A","url":"https://www.omim.org/entry/611464"},{"mim_id":"608954","title":"MON1 HOMOLOG B, SECRETORY TRAFFICKING-ASSOCIATED; MON1B","url":"https://www.omim.org/entry/608954"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Vesicles","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CCZ1"},"hgnc":{"alias_symbol":["CGI-43","CCZ1A"],"prev_symbol":["C7orf28A"]},"alphafold":{"accession":"P86791","domains":[{"cath_id":"3.30.450.70","chopping":"16-184","consensus_level":"high","plddt":94.4431,"start":16,"end":184},{"cath_id":"3.30.450.30","chopping":"199-263_277-366","consensus_level":"high","plddt":92.3156,"start":199,"end":366},{"cath_id":"3.30.450","chopping":"375-474","consensus_level":"high","plddt":86.8175,"start":375,"end":474}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P86791","model_url":"https://alphafold.ebi.ac.uk/files/AF-P86791-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P86791-F1-predicted_aligned_error_v6.png","plddt_mean":88.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCZ1","jax_strain_url":"https://www.jax.org/strain/search?query=CCZ1"},"sequence":{"accession":"P86791","fasta_url":"https://rest.uniprot.org/uniprotkb/P86791.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P86791/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P86791"}},"corpus_meta":[{"pmid":"20797862","id":"PMC_20797862","title":"The Mon1-Ccz1 complex is the GEF of the late endosomal Rab7 homolog Ypt7.","date":"2010","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/20797862","citation_count":319,"is_preprint":false},{"pmid":"27559127","id":"PMC_27559127","title":"The Ccz1-Mon1-Rab7 module and Rab5 control distinct steps of autophagy.","date":"2016","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/27559127","citation_count":169,"is_preprint":false},{"pmid":"29038162","id":"PMC_29038162","title":"Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux.","date":"2017","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29038162","citation_count":105,"is_preprint":false},{"pmid":"12364329","id":"PMC_12364329","title":"The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery 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cell","url":"https://pubmed.ncbi.nlm.nih.gov/24623720","citation_count":51,"is_preprint":false},{"pmid":"11590240","id":"PMC_11590240","title":"The Ccz1 protein interacts with Ypt7 GTPase during fusion of multiple transport intermediates with the vacuole in S. cerevisiae.","date":"2001","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/11590240","citation_count":46,"is_preprint":false},{"pmid":"26627821","id":"PMC_26627821","title":"Mon1-Ccz1 activates Rab7 only on late endosomes and dissociates from the lysosome in mammalian cells.","date":"2015","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/26627821","citation_count":40,"is_preprint":false},{"pmid":"34432599","id":"PMC_34432599","title":"C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during 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chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36649906","citation_count":19,"is_preprint":false},{"pmid":"26471407","id":"PMC_26471407","title":"The Ccz1 mediates the autophagic clearance of damaged mitochondria in response to oxidative stress in Candida albicans.","date":"2015","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/26471407","citation_count":18,"is_preprint":false},{"pmid":"35589873","id":"PMC_35589873","title":"The lysosomal V-ATPase a3 subunit is involved in localization of Mon1-Ccz1, the GEF for Rab7, to secretory lysosomes in osteoclasts.","date":"2022","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/35589873","citation_count":16,"is_preprint":false},{"pmid":"20709422","id":"PMC_20709422","title":"Mutants of the Saccharomyces cerevisiae VPS genes CCZ1 and YPT7 are blocked in different stages of sporulation.","date":"2010","source":"European journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20709422","citation_count":16,"is_preprint":false},{"pmid":"37155863","id":"PMC_37155863","title":"Structure of the metazoan Rab7 GEF complex Mon1-Ccz1-Bulli.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37155863","citation_count":15,"is_preprint":false},{"pmid":"37880247","id":"PMC_37880247","title":"Identification of CCZ1 as an essential lysosomal trafficking regulator in Marburg and Ebola virus infections.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37880247","citation_count":12,"is_preprint":false},{"pmid":"21155714","id":"PMC_21155714","title":"CCZ1, MON1 and YPT7 genes are involved in pexophagy, the Cvt pathway and non-specific macroautophagy in the methylotrophic yeast Pichia pastoris.","date":"2011","source":"Cell biology 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/19700218","citation_count":5,"is_preprint":false},{"pmid":"35793146","id":"PMC_35793146","title":"VmMon1-Ccz1 Complex Is Required for Conidiation, Autophagy, and Virulence in Valsa mali.","date":"2022","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/35793146","citation_count":3,"is_preprint":false},{"pmid":"39062041","id":"PMC_39062041","title":"CCZ1 Accelerates the Progression of Cervical Squamous Cell Carcinoma by Promoting MMP2/MMP17 Expression.","date":"2024","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/39062041","citation_count":2,"is_preprint":false},{"pmid":"40864718","id":"PMC_40864718","title":"Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.","date":"2025","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/40864718","citation_count":1,"is_preprint":false},{"pmid":"41943871","id":"PMC_41943871","title":"Endosomal maturation is controlled by the trimeric Bulli-Mon1-Ccz1 Rab7 GEF complex and the Rab5 GTPase-activating protein GAPsec.","date":"2026","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/41943871","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.27.645700","title":"Mechanistic Plasticity of the RabGEFs Mon1-Ccz1 and Fuzzy-Inturned","date":"2025-03-28","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.27.645700","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16239,"output_tokens":4912,"usd":0.061199,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13052,"output_tokens":4607,"usd":0.090218,"stage2_stop_reason":"end_turn"},"total_usd":0.151417,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"The dimeric Mon1-Ccz1 complex is the guanine nucleotide exchange factor (GEF) for the late endosomal Rab7 homolog Ypt7. The complex, but neither protein alone, counteracts GAP function in vivo, rescues in vitro fusion of vacuoles carrying Ypt7-GDP, and promotes nucleotide exchange on Ypt7 independently of Vps39/HOPS.\",\n      \"method\": \"In vitro nucleotide exchange assay, in vitro vacuole fusion assay, in vivo GAP suppression assay\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of GEF activity, multiple orthogonal assays, widely replicated across subsequent studies\",\n      \"pmids\": [\"20797862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Mon1 and Ccz1 physically interact as a stable protein complex (the Ccz1-Mon1 complex), function in nearly all membrane-trafficking pathways targeting the vacuole, and act after transport vesicle formation but before or at the fusion step with the vacuole. The complex peripherally associates with a perivacuolar compartment.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, fluorescence microscopy, genetic deletion analysis with multiple pathway readouts (Cvt, autophagy, pexophagy, CPY/ALP/MVB pathways)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, fractionation, multiple orthogonal pathway assays, replicated in subsequent work\",\n      \"pmids\": [\"12364329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"The Ccz1-Mon1 complex is required for the tethering/docking stage of homotypic vacuole fusion. In its absence, SNARE pairing integrity and the class C Vps/HOPS complex interaction with unpaired SNAREs are both impaired. The complex co-localizes with other fusion components on the vacuole as part of the cis-SNARE complex, and its vacuolar association is regulated by the class C Vps/HOPS complex.\",\n      \"method\": \"In vitro homotypic vacuole fusion assay, SNARE co-immunoprecipitation, fluorescence co-localization, genetic analysis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reconstituted in vitro fusion assay, biochemical SNARE interaction studies, multiple orthogonal methods\",\n      \"pmids\": [\"14662743\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Ccz1 physically interacts with the Rab GTPase Ypt7. Extragenic suppressors of CCZ1 deletion all mapped to mutated alleles of YPT7 (with mutations in the guanine-binding domains), and direct physical interaction was confirmed by co-immunoprecipitation.\",\n      \"method\": \"Suppressor genetics, co-immunoprecipitation\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus co-IP, single lab, two orthogonal methods\",\n      \"pmids\": [\"11590240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Mon1-Ccz1 is recruited to endosomes and vacuoles through binding to phosphatidylinositol 3-phosphate (PI3P). After activating Ypt7, Mon1 is phosphorylated by the type 1 casein kinase Yck3 and released from vacuoles for recycling. Phosphorylation-site mutants of Mon1 are retained on vacuoles, and this retention is rescued by addition of recombinant Yck3.\",\n      \"method\": \"Lipid competition assay (PI3P), recombinant kinase add-back assay, phosphomutant analysis, vacuole membrane binding assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro lipid binding, recombinant kinase reconstitution, mutagenesis; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"24623720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Mon1-Ccz1 is specifically recruited to the pre-autophagosomal structure under starvation by directly binding Atg8 (yeast LC3 homolog) via at least one LIR motif in the Ccz1 C-terminus. This LIR motif is essential for autophagy but not for endosomal transport. Only wild-type, not LIR-mutated Mon1-Ccz1, promotes Atg8-dependent activation of Ypt7.\",\n      \"method\": \"LIR motif mutagenesis, in vitro binding assay, GEF activity assay, fluorescence microscopy, yeast genetics\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mutagenesis, in vitro binding and GEF assays, multiple orthogonal methods in single study\",\n      \"pmids\": [\"29446751\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The Ccz1-Mon1-Rab7 module is required for autophagosome-lysosome fusion in Drosophila fat cells. Rab5 is dispensable for the Ccz1-Mon1-dependent recruitment of Rab7 to PI3P-positive autophagosomes (which are generated by Atg14-containing Vps34 PI3 kinase complex), placing the Ccz1-Mon1 complex downstream of PI3P generation and upstream of autophagosome-lysosome fusion.\",\n      \"method\": \"Genetic loss-of-function (Drosophila mutants), fluorescence microscopy, autophagosome quantification, epistasis analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with defined phenotypic readout, multiple mutant combinations tested, single lab\",\n      \"pmids\": [\"27559127\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Mon1-Ccz1 activates Rab7 specifically on late endosomes in mammalian cells; Rab7 activity on lysosomes is independent of Mon1-Ccz1. Mon1-Ccz1 dissociates from lysosomes after late endosome-lysosome fusion. Active Rab7 on lysosomes (independent of Mon1-Ccz1) plays a role in perinuclear lysosome clustering.\",\n      \"method\": \"FRET-based Rab7 activity sensor, confocal FRET imaging, siRNA knockdown of Mon1-Ccz1, EGF-induced macropinocytosis assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — FRET biosensor with knockdown, single lab, two orthogonal approaches\",\n      \"pmids\": [\"26627821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"C18orf8/RMC1 is a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor complex and positively regulates RAB7 recruitment to late endosomes/autophagosomes. This was identified through interaction proteomics of proteins accumulating in GABARAP/L1/L2-deficient cells.\",\n      \"method\": \"Interaction proteomics (AP-MS), genetic cell engineering (ATG8 knockouts), quantitative autophagosome proteomics\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — AP-MS identification with functional validation in KO cells, single lab\",\n      \"pmids\": [\"29038162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"C5orf51 is a component of the MON1-CCZ1 complex, identified as an interactor of GDP-locked RAB7A by proximity biotinylation. In the absence of C5orf51, RAB7A localization on depolarized mitochondria is compromised and RAB7A is degraded by the proteasome, indicating C5orf51 stabilizes RAB7A and supports its mitochondrial recruitment during mitophagy.\",\n      \"method\": \"Proximity-dependent biotinylation (miniTurbo), co-immunoprecipitation, knockout cell analysis, fluorescence microscopy\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity biotinylation plus Co-IP plus KO phenotype, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"34432599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The lysosomal V-ATPase a3 subunit interacts with the Mon1A-Ccz1 complex (GEF for Rab7) via the amino-terminal half domain of a3 and the longin motifs of Mon1A and Ccz1. This interaction is required for Mon1A-Ccz1 localization to secretory lysosomes in osteoclasts, which mediates Rab7 recruitment to the organelle.\",\n      \"method\": \"Co-immunoprecipitation in HEK293T cells, domain mapping by truncation mutants, endogenous Ccz1 localization analysis in a3-knockout osteoclasts\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping plus KO localization phenotype, single lab\",\n      \"pmids\": [\"35589873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM structure of the metazoan Mon1-Ccz1-Bulli (MCBulli) complex was solved at 3.2 Å resolution. Bulli associates as a leg-like extension at the periphery of the Mon1-Ccz1 heterodimer and does not impact GEF activity or interactions with recruiter/substrate GTPases, but likely serves as a recruitment platform for additional regulators of endolysosomal trafficking.\",\n      \"method\": \"Cryo-electron microscopy (3.2 Å), structural analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution cryo-EM structure with functional interpretation; single study but rigorous structural method\",\n      \"pmids\": [\"37155863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"An amphipathic helix in Ccz1 is required for Mon1-Ccz1 function in autophagy but not endosomal maturation, revealing a mechanism for differential targeting to autophagosomes vs. endosomes. The Ccz1 amphipathic helix interacts with lipid packing defects, Mon1 basic patches bind positively charged lipids, and association with recruiter proteins synergistically governs membrane recruitment. Interaction with recruiter proteins can further stimulate GEF activity beyond membrane concentration effects.\",\n      \"method\": \"Mutagenesis, lipid-binding assays, in vitro GEF activity assays, yeast functional genetics\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mutagenesis, in vitro lipid and GEF assays, multiple orthogonal methods in single study\",\n      \"pmids\": [\"36649906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CCZ1 controls early-to-late endosomal trafficking of Marburg and Ebola filoviruses, functioning as an essential host factor in the early stage of filovirus replication. Loss of CCZ1 nearly completely abolishes Marburg and Ebola infections, validated in 3D primary human hepatocyte cultures and blood-vessel organoids.\",\n      \"method\": \"Haploid cell genetic screen, CCZ1 knockout validation, 3D primary human tissue models (hepatocyte cultures, blood-vessel organoids), viral infection assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic screen plus KO validation in multiple cell/tissue models, single study\",\n      \"pmids\": [\"37880247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CCZ1-MON1A complex dysfunction causes decreased active RAB7 on autophagosome fractions in Alzheimer's disease models. Overexpressing CCZ1-MON1A increases active RAB7, enhances autophagosome maturation, and promotes degradation of APP-CTFs, Aβ, and P-tau in an autophagy-dependent manner.\",\n      \"method\": \"Autophagosome fractionation, GST-R7BD affinity isolation assay for GTP-RAB7, AAV-mediated overexpression in mouse brain, immunoblotting\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical GEF activity assay on isolated autophagosomes, in vivo AAV overexpression, multiple readouts; single lab\",\n      \"pmids\": [\"35198070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Structural and biochemical comparison of Mon1-Ccz1 and Fuzzy-Inturned reveals that both tri-longin domain GEF complexes use a conserved sequence motif of their substrate GTPases for catalysis, while secondary interactions mediate target discrimination. The metazoan RMC1/Bulli subunit mediates membrane recruitment of the Mon1-Ccz1 GEF complex via electrostatic interactions through a distinct interface from the fungal dimer, demonstrated by protein-lipid interaction studies and functional characterization in flies.\",\n      \"method\": \"Structural determination, protein-lipid interaction assays, in vitro reconstitution, functional genetics in Drosophila\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — structural analysis combined with in vitro reconstitution, lipid interaction assays, and in vivo functional genetics; multiple orthogonal methods\",\n      \"pmids\": [\"40864718\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In C. elegans, CCZ-1 mediates digestion of apoptotic corpses by acting in phagosome maturation through recruitment of the GTPase RAB-7 to phagosomes, placing CCZ-1 upstream of RAB-7 in the phagosome maturation pathway.\",\n      \"method\": \"Genetic loss-of-function (C. elegans deletion mutants), fluorescence microscopy of corpse persistence and RAB-7 recruitment\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotype and RAB-7 localization readout, single lab\",\n      \"pmids\": [\"20519582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In C. elegans, CCZ-1 functions independently of SAND-1 (Mon1 ortholog) in gut granule (lysosome-related organelle) biogenesis, possibly acting with GLO-3 as a GEF for the Rab32/38-related GTPase GLO-1. Point mutations in GLO-1 predicted to increase spontaneous nucleotide exchange suppress loss of gut granules by ccz-1 mutants, genetically placing CCZ-1 upstream of GLO-1.\",\n      \"method\": \"Genetic epistasis (suppressor analysis), fluorescence microscopy, C. elegans mutant analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — genetic suppressor screen suggesting CCZ-1/GLO-3 as GLO-1 GEF, but GEF activity not directly demonstrated in vitro; single lab\",\n      \"pmids\": [\"24501423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The trimeric Bulli-Mon1-Ccz1 Rab7 GEF complex (BuMC1-GEF) interacts with Rab5, which stimulates its GEF activity during endosomal maturation in Drosophila nephrocytes. GAPsec is identified as a GAP for Rab5 required for endosomal maturation; its inactivation results in enlarged dysfunctional endosomes unable to fuse with lysosomes.\",\n      \"method\": \"Drosophila genetic loss-of-function, fluorescence microscopy of endosomal trafficking, biochemical interaction analysis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Drosophila genetics with defined trafficking phenotype and biochemical GEF-stimulation data; single study\",\n      \"pmids\": [\"41943871\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCZ1 forms an obligate heterodimer with MON1 (and, in metazoans, a trimeric complex additionally containing RMC1/Bulli) that functions as the guanine nucleotide exchange factor (GEF) for Rab7/Ypt7, activating it specifically on late endosomes and autophagosomes to drive endosomal maturation and autophagosome-lysosome fusion; the complex is recruited to membranes through a synergistic code of PI3P binding, interaction with Atg8/LC3 (via a Ccz1 LIR motif, for autophagy-specific targeting), and electrostatic lipid interactions via a Ccz1 amphipathic helix, and its membrane association is dynamically regulated by phosphorylation of Mon1 by the casein kinase Yck3, which promotes release and recycling after Rab7 activation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCZ1 is an obligate subunit of a membrane-trafficking guanine nucleotide exchange factor (GEF) that drives endosomal maturation and autophagosome-lysosome fusion by activating the late-endosomal Rab7/Ypt7 GTPase [#0, #1]. CCZ1 forms a stable heterodimer with MON1, and only the assembled complex—not either protein alone—catalyzes nucleotide exchange on Ypt7, counteracts GAP activity, and rescues vacuole fusion [#0]; CCZ1 itself contacts the substrate GTPase Ypt7 directly [#3]. The complex acts at the tethering/docking stage of homotypic fusion, where its membrane association is governed by the HOPS/class C Vps machinery [#2]. Membrane recruitment follows a synergistic code: binding to PI3P [#4], an autophagy-specific LIR motif in the CCZ1 C-terminus that engages Atg8/LC3 to target pre-autophagosomal structures [#5], and a CCZ1 amphipathic helix that reads lipid-packing defects and selectively supports autophagy over endosomal maturation [#12]. After activating Rab7, MON1 is phosphorylated by the casein kinase Yck3, releasing the complex from the membrane for recycling [#4]. In metazoans the complex acquires a third subunit, RMC1/Bulli, which forms a peripheral leg-like extension serving as a recruitment platform and contributing electrostatic membrane binding without altering core GEF catalysis [#8, #11, #15]. The complex functions across endosomal maturation, autophagy, mitophagy, and phagosome maturation [#6, #7, #9, #16], and CCZ1 is an essential host factor for early-to-late endosomal trafficking of Ebola and Marburg filoviruses [#13]. Restoring CCZ1-MON1A activity enhances Rab7-dependent autophagosome maturation and clearance of APP-CTFs, Aβ, and P-tau in Alzheimer's disease models [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that CCZ1 physically engages the Rab GTPase Ypt7 connected the previously orphan CCZ1 to Rab7-dependent membrane fusion.\",\n      \"evidence\": \"suppressor genetics mapping CCZ1-deletion suppressors to YPT7 alleles, plus co-immunoprecipitation in yeast\",\n      \"pmids\": [\"11590240\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish whether CCZ1 acts catalytically on Ypt7 or merely binds it\", \"Role of a CCZ1 partner not yet defined\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defining MON1 and CCZ1 as a stable complex acting after vesicle formation but before vacuolar fusion placed the complex at a discrete trafficking step across multiple pathways.\",\n      \"evidence\": \"reciprocal Co-IP, subcellular fractionation, and deletion analysis across Cvt, autophagy, pexophagy and MVB/CPY/ALP pathways in yeast\",\n      \"pmids\": [\"12364329\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular activity of the complex not yet identified\", \"Mechanism of perivacuolar recruitment unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Localizing CCZ1-MON1 function to the tethering/docking stage of homotypic fusion tied the complex to SNARE pairing and HOPS-regulated membrane association.\",\n      \"evidence\": \"in vitro homotypic vacuole fusion assay, SNARE Co-IP, and co-localization in yeast\",\n      \"pmids\": [\"14662743\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not yet define the biochemical activity (GEF) underlying the fusion defect\", \"Causal order between HOPS and CCZ1-MON1 incompletely resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Reconstituting GEF activity demonstrated that the MON1-CCZ1 dimer—not either protein alone—is the nucleotide exchange factor for Ypt7/Rab7, defining the complex's core biochemical function.\",\n      \"evidence\": \"in vitro nucleotide exchange assay, in vitro vacuole fusion rescue, and in vivo GAP suppression; parallel C. elegans phagosome maturation genetics\",\n      \"pmids\": [\"20797862\", \"20519582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address how the complex is targeted to specific membranes\", \"Did not resolve autophagy- versus endosome-specific functions\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying PI3P binding and Yck3-dependent phosphorylation revealed how the GEF is recruited to and subsequently released from membranes, defining a recruitment-recycling cycle.\",\n      \"evidence\": \"PI3P lipid competition, recombinant Yck3 add-back, and phosphomutant membrane-binding assays in yeast\",\n      \"pmids\": [\"24623720\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not explain how recruitment is made autophagy-specific\", \"Phospho-regulation tested in yeast only\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"FRET sensing in mammalian cells showed MON1-CCZ1 activates Rab7 specifically on late endosomes, with lysosomal Rab7 activity controlled by a distinct, complex-independent mechanism, refining the spatial logic of Rab7 activation.\",\n      \"evidence\": \"FRET-based Rab7 biosensor with siRNA knockdown and EGF-induced macropinocytosis in mammalian cells\",\n      \"pmids\": [\"26627821\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The MON1-CCZ1-independent lysosomal Rab7 activator not identified\", \"Single biosensor approach in one lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Drosophila genetics positioned the CCZ1-MON1-Rab7 module downstream of PI3P generation and upstream of autophagosome-lysosome fusion, independent of Rab5.\",\n      \"evidence\": \"loss-of-function mutants, autophagosome quantification, and epistasis in fly fat cells\",\n      \"pmids\": [\"27559127\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the molecular recruiter linking PI3P-positive autophagosomes to the complex\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovery of RMC1/C18orf8 as a metazoan-specific subunit expanded the dimeric GEF into a trimeric complex that promotes Rab7 recruitment.\",\n      \"evidence\": \"interaction proteomics from GABARAP/L1/L2-deficient cells and functional validation in ATG8 knockouts\",\n      \"pmids\": [\"29038162\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural placement and catalytic contribution of RMC1 not yet defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defining a CCZ1 LIR motif that binds Atg8 explained how the complex is targeted specifically to pre-autophagosomal structures, separating autophagic from endosomal recruitment.\",\n      \"evidence\": \"LIR mutagenesis, in vitro binding and GEF assays, and microscopy in yeast\",\n      \"pmids\": [\"29446751\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether LIR-mediated targeting operates identically in metazoans not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identifying C5orf51 as a complex component linked MON1-CCZ1 to RAB7A stabilization and mitochondrial recruitment during mitophagy.\",\n      \"evidence\": \"miniTurbo proximity biotinylation with GDP-locked RAB7A, Co-IP, and knockout phenotyping in mammalian cells\",\n      \"pmids\": [\"34432599\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relationship between C5orf51 and RMC1 within the complex unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Mapping the V-ATPase a3 interaction and demonstrating CCZ1-MON1A's role in Alzheimer's models connected the GEF to organelle-specific recruitment and to neurodegenerative proteostasis.\",\n      \"evidence\": \"Co-IP with domain mapping in HEK293T and a3-knockout osteoclasts; autophagosome fractionation and AAV overexpression in mouse brain\",\n      \"pmids\": [\"35589873\", \"35198070\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct GEF deficit in disease vs. compensatory effect not fully separated\", \"Longin-domain/a3 interaction tested in limited cell types\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Cryo-EM of the trimeric MCBulli complex and dissection of the CCZ1 amphipathic helix resolved the architecture and the dual lipid-/recruiter-based membrane code that distinguishes autophagic from endosomal targeting.\",\n      \"evidence\": \"3.2 Å cryo-EM, lipid-binding and in vitro GEF assays with mutagenesis, plus a haploid screen identifying CCZ1 as an essential filovirus host factor\",\n      \"pmids\": [\"37155863\", \"36649906\", \"37880247\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulators recruited via the Bulli leg not identified\", \"How amphipathic helix and PI3P binding are coordinated in vivo unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Comparative structural and biochemical analysis showed tri-longin GEFs share a conserved substrate-recognition motif while secondary interactions confer target specificity, and that metazoan RMC1/Bulli supplies electrostatic membrane recruitment through a distinct interface.\",\n      \"evidence\": \"structural determination, protein-lipid interaction assays, in vitro reconstitution, and Drosophila functional genetics\",\n      \"pmids\": [\"40864718\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full set of secondary interactions governing in vivo specificity not enumerated\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrating that Rab5 directly stimulates the trimeric Rab7 GEF positioned the complex within a Rab5-to-Rab7 conversion switch during endosomal maturation.\",\n      \"evidence\": \"Drosophila nephrocyte genetics, trafficking microscopy, and biochemical GEF-stimulation analysis\",\n      \"pmids\": [\"41943871\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis of Rab5-mediated GEF stimulation not structurally defined\", \"Single study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the distinct recruitment modules (PI3P, Atg8/LIR, amphipathic helix, RMC1/Bulli electrostatics, V-ATPase a3, Rab5) are integrated to select among endosomal, autophagic, mitophagic, and phagosomal targets in a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified in vivo model of compartment-selective recruitment\", \"Regulators docking on the Bulli platform unidentified\", \"Mammalian counterpart of Yck3 phospho-recycling not characterized in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 5, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 15]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4, 12, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [7, 16]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [7, 10]},\n      {\"term_id\": \"GO:0005773\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5, 6, 9, 14]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 2, 7]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"complexes\": [\"MON1-CCZ1 GEF complex\", \"MON1-CCZ1-RMC1/Bulli (MCBulli) trimeric complex\"],\n    \"partners\": [\"MON1\", \"RMC1\", \"YPT7\", \"RAB7A\", \"C5orf51\", \"ATG8\", \"TCIRG1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":8,"faith_pct":87.5}}