{"gene":"VPS29","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1997,"finding":"VPS29 (yeast) is required for endosome-to-Golgi retrieval of the vacuolar sorting receptor Vps10p; in vps29 mutants, Vps10p mislocalizes from the Golgi to the vacuolar membrane, indicating VPS29 functions in retrograde recycling of cargo receptors from the prevacuolar endosome back to the Golgi.","method":"Genetic loss-of-function (yeast vps29 mutants), subcellular fractionation, CPY secretion assay","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with defined cargo-sorting phenotype, subcellular fractionation, replicated across multiple VPS gene mutants in same study; foundational paper replicated by many subsequent studies","pmids":["9105038"],"is_preprint":false},{"year":2005,"finding":"Crystal structure of mammalian VPS29 reveals a phosphoesterase fold with structural similarity to divalent metal-containing phosphoesterases; VPS29 has no detectable phosphoesterase activity in vitro. VPS29 and VPS26 bind independently to VPS35 to form a high-affinity heterotrimeric subcomplex. A conserved hydrophobic surface on VPS29 (distinct from the VPS35-binding site) mediates assembly with sorting nexins in yeast; mutations at either binding site cause defects in retromer-dependent membrane trafficking.","method":"X-ray crystallography, in vitro phosphatase assay, mutagenesis, binding/assembly assays, in vivo trafficking assay","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis plus in vitro activity assay plus in vivo functional validation; multiple orthogonal methods in single rigorous study","pmids":["15965486"],"is_preprint":false},{"year":2006,"finding":"Recombinant human VPS29 displays in vitro phosphatase activity toward a serine-phosphorylated peptide from the acidic-cluster dileucine motif of the CI-M6PR cytoplasmic tail; activity requires co-presence of VPS26 and VPS35, is abolished by alanine substitution of active-site metal-coordinating residues, and depends on zinc (VPS29 binds Zn²⁺ as shown by ICP-MS; activity is abrogated by zinc chelators and restored by ZnCl₂).","method":"In vitro phosphatase assay with recombinant proteins, active-site mutagenesis, ICP-MS metal analysis, metal chelation experiments","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — rigorous in vitro biochemistry with mutagenesis and metal analysis, but single lab; result partially contradicted by Swarbrick et al. 2011","pmids":["16737443"],"is_preprint":false},{"year":2011,"finding":"VPS29 is not a functional metalloenzyme: despite coordinating Mn²⁺ and Zn²⁺ in the putative active site, affinity for metals is low and no phosphatase activity is detected toward a putative peptide substrate. NMR/ITC and RDC measurements show VPS29 is a rigid scaffold with metal-independent conformation. NMR chemical shift mapping demonstrates VPS29 associates with SNX1 via a conserved hydrophobic surface, but with low affinity requiring additional interactions in vivo.","method":"X-ray crystallography, NMR spectroscopy (RDC, chemical shift mapping), ITC, in vitro phosphatase assay","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal structural and biophysical methods (X-ray, NMR RDC, ITC, enzyme assay) in a single rigorous study; directly contradicts and supersedes phosphatase activity claim from Damen et al. 2006","pmids":["21629666"],"is_preprint":false},{"year":2010,"finding":"VPS29 deficiency leads to degradation of VPS35 (and vice versa), but VPS26 deficiency does not affect VPS29 or VPS35 levels. The VPS29-VPS35 sub-complex is more stable than the VPS26-VPS35 sub-complex in vitro, and the VPS26-VPS35 sub-complex is more susceptible to ubiquitin-proteasome-mediated degradation, indicating VPS29 stabilizes VPS35 as a biologically stable intermediate during retromer assembly.","method":"siRNA knockdown, in vitro complex formation, ubiquitin-proteasome inhibitor treatment, immunoblotting","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro reconstitution combined with cellular KD, single lab with two orthogonal approaches","pmids":["25937119"],"is_preprint":false},{"year":2017,"finding":"The Legionella effector RidL binds the VPS29 retromer subunit through a protruding β-hairpin containing Ile170; this interaction displaces the Rab7 GAP TBC1D5 from VPS29 and from Legionella-containing vacuoles, blocking retrograde vesicle trafficking and promoting intracellular bacterial replication. Deletion of the β-hairpin or substitution of Ile170 (RidL) or Leu152 (VPS29) abolishes the interaction in cells and in vitro.","method":"Crystal structure of RidL-VPS29 complex, mutagenesis, co-immunoprecipitation in eukaryotic cells, in vitro binding assays, intracellular replication assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis plus cellular and in vitro binding validation plus functional replication assay; multiple orthogonal methods","pmids":["29146912"],"is_preprint":false},{"year":2020,"finding":"VARP contains a 12-residue, four-cysteine Zn-fingernail microdomain that binds the same hydrophobic site on VPS29 as TBC1D5; VARP and TBC1D5 compete for VPS29 binding in vivo. Mutations abolishing VPS29:VARP binding inhibit trafficking from endosomes to the cell surface. In assembled retromer arches, the geometry of VPS29 subunits favors VARP binding to two VPS29 subunits simultaneously.","method":"NMR spectroscopy, X-ray crystallography, mutagenesis, in vivo competition assays, endosomal trafficking assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR + X-ray structure of VPS29:VARP complex, mutagenesis, and in vivo functional validation with multiple orthogonal methods","pmids":["33024112"],"is_preprint":false},{"year":2020,"finding":"In Drosophila, Vps29 is required for correct localization of retromer (Vps35/Vps26) in neurons: in Vps29 mutants, Vps35 and Vps26 remain associated but retromer mislocalizes from neuropil to soma together with Rab7. Vps29 mutant phenotypes (impaired synaptic transmission, locomotion defects, endolysosomal dysfunction) are suppressed by reducing Rab7 or overexpressing the Rab7 GAP TBC1D5, placing VPS29 upstream of Rab7 regulation in the retromer pathway.","method":"Drosophila genetics (loss-of-function, epistasis), immunofluorescence/localization, electrophysiology, behavioral assays, electron microscopy","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic loss-of-function with epistasis (suppressor by Rab7 reduction and TBC1D5 overexpression), multiple orthogonal phenotypic readouts, localization experiments with functional consequences","pmids":["32286230"],"is_preprint":false},{"year":2022,"finding":"VPS29 deficiency in human lung cells causes changes in endosome morphology and acidity and attenuates endosomal protease activity, trapping incoming coronavirus (HCoV-OC43, SARS-CoV-2) particles in endosomes and reducing infection. VPS29 loss had no effect on influenza A endosomal entry and enhanced influenza A infection, demonstrating opposing roles of VPS29-dependent endosome regulation on different viruses.","method":"Genome-wide CRISPR loss-of-function screen, genetic validation (VPS29 KO), viral infection assays, endosome morphology and acidity measurements, endosomal protease activity assay","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with multiple viral infection phenotypes and endosomal functional assays; single lab, but multiple orthogonal cellular readouts","pmids":["35229640"],"is_preprint":false},{"year":2024,"finding":"VPS29 directly binds a peptide fragment of the WASH complex subunit FAM21 via a conserved hydrophobic pocket on VPS29; the crystal structure shows FAM21 adopts a sharp bend to insert into this pocket using the same binding mode as other VPS29 effectors (e.g., RidL, TBC1D5, VARP). This interaction is distinct from VPS35:FAM21 contacts. The Parkinson's disease-linked VPS35 D620N mutation does not significantly impair direct FAM21 association in vitro.","method":"Crystal structure of VPS29:FAM21 peptide complex, in vitro binding assays, mutagenesis","journal":"Protein science : a publication of the Protein Society","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with in vitro binding validation; single lab but rigorous structural method","pmids":["38607248"],"is_preprint":false},{"year":2025,"finding":"A third VPS29 isoform (VPS29C) harbors an extended N-terminal sequence that constitutes an autoinhibitory domain blocking the hydrophobic groove required for effector recruitment to Retromer and for association with Retriever and Commander complexes. VPS29C is therefore uniquely able to uncouple Retromer-dependent cargo sorting from broader VPS29A/B roles in accessory protein recruitment.","method":"AlphaFold structural modeling, in vitro complex reconstitution, mass spectrometry, molecular cell biology","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro reconstitution plus mass spectrometry plus cell biology; single lab; novel isoform identification with functional characterization","pmids":["40587794"],"is_preprint":false},{"year":2013,"finding":"In C. elegans, loss of vps-29 (cargo-selective retromer subunit) disrupts Wls recycling from endosomes to TGN, impairing Wnt secretion; this defect can be rescued by blocking late endosomal maturation, which accumulates Wls in late endosomes where it can be retrieved via an SNX-BAR-dependent retromer pathway, demonstrating that the VPS29-containing cargo-selective subcomplex preferentially acts at an early endosomal station distinct from the SNX-BAR pathway.","method":"C. elegans genetics (vps-29 loss-of-function), Wnt secretion assay, pharmacological inhibition of endosomal maturation, fluorescence microscopy","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic KO with defined cargo-sorting phenotype and pharmacological epistasis; single lab with two complementary approaches","pmids":["24056045"],"is_preprint":false},{"year":2024,"finding":"VARP directly interacts with SNX27 PDZ domain via its N-terminus, and VARP is required to reconstitute an endosomal supercomplex containing SNX27, ESCPE-1, and Retromer (VPS26/VPS35/VPS29) on PI(3)P-enriched membranes in a fully reconstituted biochemical system; specific point mutations in VARP abolish the VARP:SNX27 interaction in vitro.","method":"Biochemical reconstitution with purified mammalian proteins, AlphaFold2 Multimer modeling, liposome tubulation assay, in vitro binding assays, mutagenesis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — rigorous in vitro reconstitution with mutagenesis but preprint, single lab; provides mechanistic insight into VPS29-containing supercomplex assembly on membranes","pmids":[],"is_preprint":true},{"year":2024,"finding":"ATG5 associates with retromer core components VPS26, VPS29, and VPS35; knockout of ATG5 or other genes essential for membrane atg8ylation impairs retromer-dependent sorting of GLUT1 to the plasma membrane, independently of canonical autophagy, revealing a noncanonical role for membrane atg8ylation in retromer assembly and function.","method":"Co-immunoprecipitation, ATG5/atg8ylation gene knockouts, GLUT1 trafficking assay","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and KO with defined trafficking phenotype, but preprint and single lab; mechanistic link between atg8ylation and VPS29/retromer function is preliminary","pmids":[],"is_preprint":true}],"current_model":"VPS29 is a structurally rigid, phosphoesterase-fold scaffold subunit of the retromer heterotrimer (VPS26/VPS35/VPS29) that stabilizes the VPS29-VPS35 core, recruits accessory proteins (TBC1D5, VARP, FAM21/WASH complex, SNX1) via a conserved hydrophobic surface, controls Rab7 activity and retromer localization in neurons, and thereby mediates endosome-to-Golgi/TGN retrograde retrieval of transmembrane cargo receptors; whether VPS29 has intrinsic phosphatase activity remains contested, but the consensus favors a non-enzymatic scaffolding function."},"narrative":{"mechanistic_narrative":"VPS29 is a core subunit of the cargo-selective retromer heterotrimer (VPS26/VPS35/VPS29) that mediates endosome-to-Golgi/TGN retrograde retrieval of transmembrane cargo receptors, established originally in yeast where vps29 loss mislocalizes the vacuolar sorting receptor Vps10p [PMID:9105038] and conserved across metazoa for recycling of cargoes such as Wls during Wnt secretion [PMID:24056045]. Structurally, VPS29 adopts a phosphoesterase fold but functions as a rigid, metal-independent scaffold rather than an enzyme: despite coordinating divalent metals in a putative active site, it shows no robust phosphatase activity and behaves as a conformationally stable platform [PMID:15965486, PMID:21629666]. It binds VPS35 with high affinity to form a stable VPS29-VPS35 core that protects VPS35 from proteasomal degradation, acting as a biologically stable intermediate during retromer assembly [PMID:15965486, PMID:25937119]. A single conserved hydrophobic surface on VPS29, distinct from the VPS35-binding site, serves as a hub for mutually competitive recruitment of accessory effectors—the Rab7 GAP TBC1D5, VARP, and the WASH-complex subunit FAM21—all of which engage this pocket through a shared β-hairpin/insertion binding mode, as does the Legionella effector RidL, which hijacks the site to displace TBC1D5 and block retrograde trafficking [PMID:29146912, PMID:33024112, PMID:38607248]. Through this effector hub VPS29 controls retromer localization and Rab7 activity in neurons, where its loss mislocalizes retromer and Rab7 and produces endolysosomal and synaptic defects suppressed by reducing Rab7 or boosting TBC1D5 [PMID:32286230]. VPS29-dependent control of endosome morphology, acidity, and protease activity also modulates viral entry, with opposing effects on coronaviruses versus influenza A [PMID:35229640]. An N-terminally extended VPS29C isoform autoinhibits the hydrophobic groove, uncoupling retromer cargo sorting from accessory recruitment and from association with Retriever/Commander complexes [PMID:40587794].","teleology":[{"year":1997,"claim":"Established that VPS29 is required for retrograde retrieval of cargo receptors from the endosome to the Golgi, defining its core cellular function.","evidence":"Yeast vps29 loss-of-function with subcellular fractionation and CPY secretion/Vps10p localization assays","pmids":["9105038"],"confidence":"High","gaps":["Does not define the molecular mechanism or the partner subunits in mammals","No structural basis for cargo selection"]},{"year":2005,"claim":"Resolved the VPS29 fold and assembly logic, showing it forms a high-affinity heterotrimer with VPS35/VPS26 and presents a distinct hydrophobic surface for sorting-nexin assembly, while lacking detectable enzymatic activity.","evidence":"X-ray crystallography, in vitro phosphatase assay, mutagenesis, and in vivo trafficking assays in mammalian and yeast systems","pmids":["15965486"],"confidence":"High","gaps":["Did not resolve whether the metal site has any in vivo catalytic role","Full effector repertoire of the hydrophobic surface unknown"]},{"year":2006,"claim":"Tested the hypothesis that VPS29 is a metal-dependent phosphatase, reporting Zn-dependent dephosphorylation of a CI-M6PR tail peptide requiring the assembled heterotrimer.","evidence":"In vitro phosphatase assays with recombinant VPS26/VPS35/VPS29, active-site mutagenesis, ICP-MS metal analysis, chelation","pmids":["16737443"],"confidence":"Medium","gaps":["Single lab and subsequently contradicted","No in-cell demonstration of phosphatase activity on a physiological substrate"]},{"year":2011,"claim":"Resolved the enzymatic controversy by demonstrating VPS29 is a rigid, metal-independent scaffold with no detectable phosphatase activity, recasting its role as structural rather than catalytic.","evidence":"X-ray crystallography, NMR (RDC, chemical shift mapping), ITC, and in vitro phosphatase assays","pmids":["21629666"],"confidence":"High","gaps":["Low-affinity SNX1 interaction implies additional in vivo determinants not captured in vitro"]},{"year":2010,"claim":"Showed that VPS29 stabilizes VPS35 against proteasomal degradation, explaining how the VPS29-VPS35 core is the obligate stable intermediate of retromer assembly.","evidence":"siRNA knockdown, in vitro subcomplex reconstitution, proteasome inhibition, immunoblotting","pmids":["25937119"],"confidence":"Medium","gaps":["Single lab","Mechanism of differential subcomplex stability not structurally defined"]},{"year":2017,"claim":"Revealed that the VPS29 hydrophobic surface is an exploitable effector hub by showing the Legionella effector RidL competitively displaces TBC1D5 to subvert retrograde trafficking and aid bacterial replication.","evidence":"Crystal structure of RidL:VPS29, mutagenesis, co-IP, in vitro binding, intracellular replication assays","pmids":["29146912"],"confidence":"High","gaps":["Does not establish the full set of endogenous effectors using this site","Consequences for specific cargo cohorts not mapped"]},{"year":2020,"claim":"Defined VARP as a competitive effector that binds the same VPS29 site as TBC1D5 and showed VPS29 acts upstream of Rab7 to control retromer localization in neurons.","evidence":"NMR and X-ray structures of VPS29:VARP, mutagenesis, in vivo competition and trafficking assays (mammalian); Drosophila genetics, epistasis, electrophysiology, EM","pmids":["33024112","32286230"],"confidence":"High","gaps":["How effector competition is regulated spatially/temporally is unresolved","Direct biochemical link between VPS29 and Rab7 nucleotide state not reconstituted"]},{"year":2022,"claim":"Connected VPS29-dependent endosome regulation to host susceptibility, showing its loss alters endosome morphology, acidity, and protease activity with opposing effects on coronavirus versus influenza A entry.","evidence":"Genome-wide CRISPR screen, VPS29 KO validation, viral infection assays, endosome acidity and protease assays","pmids":["35229640"],"confidence":"Medium","gaps":["Mechanism linking retromer function to endosomal protease activity not defined","Single lab"]},{"year":2024,"claim":"Showed FAM21/WASH engages the VPS29 hydrophobic pocket via the same conserved binding mode as other effectors, consolidating a unified model of effector recruitment, and that the PD-linked VPS35 D620N does not impair direct FAM21:VPS29 contact.","evidence":"Crystal structure of VPS29:FAM21 peptide complex, in vitro binding, mutagenesis","pmids":["38607248"],"confidence":"High","gaps":["Single lab","Cellular consequence of disrupting the direct VPS29:FAM21 contact not tested"]},{"year":2024,"claim":"Reconstituted a VPS29-containing endosomal supercomplex, showing VARP bridges SNX27/ESCPE-1 and retromer on PI(3)P membranes.","evidence":"Biochemical reconstitution with purified proteins, AlphaFold2 Multimer modeling, liposome tubulation, mutagenesis (preprint)","pmids":[],"confidence":"Medium","gaps":["Preprint, single lab","In-cell relevance of the reconstituted supercomplex not established"]},{"year":2025,"claim":"Identified a VPS29C isoform whose N-terminal extension autoinhibits the effector groove, providing a mechanism to uncouple retromer cargo sorting from accessory recruitment and Retriever/Commander association.","evidence":"AlphaFold modeling, in vitro complex reconstitution, mass spectrometry, cell biology","pmids":["40587794"],"confidence":"Medium","gaps":["Single lab","Physiological contexts where VPS29C is expressed and used not defined"]},{"year":null,"claim":"How effector competition at the single VPS29 hydrophobic surface is regulated in space and time to coordinate distinct trafficking routes, and how VPS29 controls Rab7 nucleotide state mechanistically, remain open.","evidence":"","pmids":[],"confidence":"High","gaps":["No reconstitution of VPS29-directed Rab7 GAP regulation","No structural model of full effector switching on assembled retromer","Isoform-specific physiology unmapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4,5,6,9]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,3,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,6,7]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,8,11,12]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0,11]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,7,11]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,8,11]}],"complexes":["retromer (VPS26/VPS35/VPS29)","WASH complex (via FAM21)","Retriever/Commander","SNX27/ESCPE-1/Retromer supercomplex"],"partners":["VPS35","VPS26","TBC1D5","VARP","FAM21","SNX1","RIDL","ATG5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UBQ0","full_name":"Vacuolar protein sorting-associated protein 29","aliases":["PEP11 homolog","Vesicle protein sorting 29"],"length_aa":182,"mass_kda":20.5,"function":"Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of the CCC subcomplex and the retriever subcomplex (PubMed:37172566, PubMed:39587083, PubMed:38062209, PubMed:38459129). Component of the retriever complex, which is a heterotrimeric complex related to retromer cargo-selective complex (CSC) and essential for retromer-independent retrieval and recycling of numerous cargos such as integrin alpha-5/beta-1 (ITGA5:ITGB1) (PubMed:28892079, PubMed:37172566, PubMed:39587083, PubMed:38062209, PubMed:38459129). Component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (PubMed:15247922, PubMed:21725319, PubMed:23563491). In the endosomes, retriever complex drives the retrieval and recycling of NxxY-motif-containing cargo proteins by coupling to SNX17, a cargo essential for the homeostatic maintenance of numerous cell surface proteins associated with processes that include cell migration, cell adhesion, nutrient supply and cell signaling (PubMed:28892079, PubMed:39587083). The recruitment of the retriever complex to the endosomal membrane involves CCC and WASH complexes (PubMed:28892079). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514) (Microbial infection) The heterotrimeric retromer cargo-selective complex (CSC) mediates the exit of human papillomavirus from the early endosome and the delivery to the Golgi apparatus","subcellular_location":"Cytoplasm; Membrane; Endosome membrane; Early endosome; Late endosome","url":"https://www.uniprot.org/uniprotkb/Q9UBQ0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS29","classification":"Not Classified","n_dependent_lines":460,"n_total_lines":1208,"dependency_fraction":0.38079470198675497},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000111237","cell_line_id":"CID001731","localizations":[{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"CCDC22","stoichiometry":10.0},{"gene":"COMMD2","stoichiometry":10.0},{"gene":"COMMD4","stoichiometry":10.0},{"gene":"VPS35","stoichiometry":10.0},{"gene":"CAPZB","stoichiometry":4.0},{"gene":"COMMD6","stoichiometry":4.0},{"gene":"CCDC93","stoichiometry":0.2},{"gene":"COMMD1","stoichiometry":0.2},{"gene":"SNX27","stoichiometry":0.2},{"gene":"SNX3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001731","total_profiled":1310},"omim":[{"mim_id":"620553","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 93; CCDC93","url":"https://www.omim.org/entry/620553"},{"mim_id":"618981","title":"VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE; VPS35L","url":"https://www.omim.org/entry/618981"},{"mim_id":"615740","title":"TBC1 DOMAIN FAMILY, MEMBER 5; TBC1D5","url":"https://www.omim.org/entry/615740"},{"mim_id":"613096","title":"SPASTIC PARAPLEGIA 36, AUTOSOMAL DOMINANT; SPG36","url":"https://www.omim.org/entry/613096"},{"mim_id":"612299","title":"COMM DOMAIN-CONTAINING PROTEIN 9; COMMD9","url":"https://www.omim.org/entry/612299"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS29"},"hgnc":{"alias_symbol":["PEP11","DC7","DC15"],"prev_symbol":[]},"alphafold":{"accession":"Q9UBQ0","domains":[{"cath_id":"3.60.21.10","chopping":"3-181","consensus_level":"high","plddt":96.5684,"start":3,"end":181}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBQ0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBQ0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBQ0-F1-predicted_aligned_error_v6.png","plddt_mean":96.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS29","jax_strain_url":"https://www.jax.org/strain/search?query=VPS29"},"sequence":{"accession":"Q9UBQ0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UBQ0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UBQ0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBQ0"}},"corpus_meta":[{"pmid":"9105038","id":"PMC_9105038","title":"Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products.","date":"1997","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/9105038","citation_count":354,"is_preprint":false},{"pmid":"17889650","id":"PMC_17889650","title":"The retromer protein VPS29 links cell polarity and organ initiation in plants.","date":"2007","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/17889650","citation_count":202,"is_preprint":false},{"pmid":"15965486","id":"PMC_15965486","title":"Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly.","date":"2005","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15965486","citation_count":128,"is_preprint":false},{"pmid":"17688404","id":"PMC_17688404","title":"Interaction of saffron carotenoids as anticancer compounds with ctDNA, Oligo (dG.dC)15, and Oligo (dA.dT)15.","date":"2007","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17688404","citation_count":75,"is_preprint":false},{"pmid":"21040701","id":"PMC_21040701","title":"Implication of mouse Vps26b-Vps29-Vps35 retromer complex in sortilin trafficking.","date":"2010","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21040701","citation_count":51,"is_preprint":false},{"pmid":"21629666","id":"PMC_21629666","title":"VPS29 is not an active metallo-phosphatase but is a rigid scaffold required for retromer interaction with accessory proteins.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21629666","citation_count":49,"is_preprint":false},{"pmid":"32286230","id":"PMC_32286230","title":"Retromer subunit, VPS29, regulates synaptic transmission and is required for endolysosomal function in the aging 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loss-of-function (yeast vps29 mutants), subcellular fractionation, CPY secretion assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with defined cargo-sorting phenotype, subcellular fractionation, replicated across multiple VPS gene mutants in same study; foundational paper replicated by many subsequent studies\",\n      \"pmids\": [\"9105038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Crystal structure of mammalian VPS29 reveals a phosphoesterase fold with structural similarity to divalent metal-containing phosphoesterases; VPS29 has no detectable phosphoesterase activity in vitro. VPS29 and VPS26 bind independently to VPS35 to form a high-affinity heterotrimeric subcomplex. A conserved hydrophobic surface on VPS29 (distinct from the VPS35-binding site) mediates assembly with sorting nexins in yeast; mutations at either binding site cause defects in retromer-dependent membrane trafficking.\",\n      \"method\": \"X-ray crystallography, in vitro phosphatase assay, mutagenesis, binding/assembly assays, in vivo trafficking assay\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis plus in vitro activity assay plus in vivo functional validation; multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"15965486\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Recombinant human VPS29 displays in vitro phosphatase activity toward a serine-phosphorylated peptide from the acidic-cluster dileucine motif of the CI-M6PR cytoplasmic tail; activity requires co-presence of VPS26 and VPS35, is abolished by alanine substitution of active-site metal-coordinating residues, and depends on zinc (VPS29 binds Zn²⁺ as shown by ICP-MS; activity is abrogated by zinc chelators and restored by ZnCl₂).\",\n      \"method\": \"In vitro phosphatase assay with recombinant proteins, active-site mutagenesis, ICP-MS metal analysis, metal chelation experiments\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous in vitro biochemistry with mutagenesis and metal analysis, but single lab; result partially contradicted by Swarbrick et al. 2011\",\n      \"pmids\": [\"16737443\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"VPS29 is not a functional metalloenzyme: despite coordinating Mn²⁺ and Zn²⁺ in the putative active site, affinity for metals is low and no phosphatase activity is detected toward a putative peptide substrate. NMR/ITC and RDC measurements show VPS29 is a rigid scaffold with metal-independent conformation. NMR chemical shift mapping demonstrates VPS29 associates with SNX1 via a conserved hydrophobic surface, but with low affinity requiring additional interactions in vivo.\",\n      \"method\": \"X-ray crystallography, NMR spectroscopy (RDC, chemical shift mapping), ITC, in vitro phosphatase assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal structural and biophysical methods (X-ray, NMR RDC, ITC, enzyme assay) in a single rigorous study; directly contradicts and supersedes phosphatase activity claim from Damen et al. 2006\",\n      \"pmids\": [\"21629666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"VPS29 deficiency leads to degradation of VPS35 (and vice versa), but VPS26 deficiency does not affect VPS29 or VPS35 levels. The VPS29-VPS35 sub-complex is more stable than the VPS26-VPS35 sub-complex in vitro, and the VPS26-VPS35 sub-complex is more susceptible to ubiquitin-proteasome-mediated degradation, indicating VPS29 stabilizes VPS35 as a biologically stable intermediate during retromer assembly.\",\n      \"method\": \"siRNA knockdown, in vitro complex formation, ubiquitin-proteasome inhibitor treatment, immunoblotting\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro reconstitution combined with cellular KD, single lab with two orthogonal approaches\",\n      \"pmids\": [\"25937119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The Legionella effector RidL binds the VPS29 retromer subunit through a protruding β-hairpin containing Ile170; this interaction displaces the Rab7 GAP TBC1D5 from VPS29 and from Legionella-containing vacuoles, blocking retrograde vesicle trafficking and promoting intracellular bacterial replication. Deletion of the β-hairpin or substitution of Ile170 (RidL) or Leu152 (VPS29) abolishes the interaction in cells and in vitro.\",\n      \"method\": \"Crystal structure of RidL-VPS29 complex, mutagenesis, co-immunoprecipitation in eukaryotic cells, in vitro binding assays, intracellular replication assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis plus cellular and in vitro binding validation plus functional replication assay; multiple orthogonal methods\",\n      \"pmids\": [\"29146912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"VARP contains a 12-residue, four-cysteine Zn-fingernail microdomain that binds the same hydrophobic site on VPS29 as TBC1D5; VARP and TBC1D5 compete for VPS29 binding in vivo. Mutations abolishing VPS29:VARP binding inhibit trafficking from endosomes to the cell surface. In assembled retromer arches, the geometry of VPS29 subunits favors VARP binding to two VPS29 subunits simultaneously.\",\n      \"method\": \"NMR spectroscopy, X-ray crystallography, mutagenesis, in vivo competition assays, endosomal trafficking assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR + X-ray structure of VPS29:VARP complex, mutagenesis, and in vivo functional validation with multiple orthogonal methods\",\n      \"pmids\": [\"33024112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In Drosophila, Vps29 is required for correct localization of retromer (Vps35/Vps26) in neurons: in Vps29 mutants, Vps35 and Vps26 remain associated but retromer mislocalizes from neuropil to soma together with Rab7. Vps29 mutant phenotypes (impaired synaptic transmission, locomotion defects, endolysosomal dysfunction) are suppressed by reducing Rab7 or overexpressing the Rab7 GAP TBC1D5, placing VPS29 upstream of Rab7 regulation in the retromer pathway.\",\n      \"method\": \"Drosophila genetics (loss-of-function, epistasis), immunofluorescence/localization, electrophysiology, behavioral assays, electron microscopy\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic loss-of-function with epistasis (suppressor by Rab7 reduction and TBC1D5 overexpression), multiple orthogonal phenotypic readouts, localization experiments with functional consequences\",\n      \"pmids\": [\"32286230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VPS29 deficiency in human lung cells causes changes in endosome morphology and acidity and attenuates endosomal protease activity, trapping incoming coronavirus (HCoV-OC43, SARS-CoV-2) particles in endosomes and reducing infection. VPS29 loss had no effect on influenza A endosomal entry and enhanced influenza A infection, demonstrating opposing roles of VPS29-dependent endosome regulation on different viruses.\",\n      \"method\": \"Genome-wide CRISPR loss-of-function screen, genetic validation (VPS29 KO), viral infection assays, endosome morphology and acidity measurements, endosomal protease activity assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with multiple viral infection phenotypes and endosomal functional assays; single lab, but multiple orthogonal cellular readouts\",\n      \"pmids\": [\"35229640\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VPS29 directly binds a peptide fragment of the WASH complex subunit FAM21 via a conserved hydrophobic pocket on VPS29; the crystal structure shows FAM21 adopts a sharp bend to insert into this pocket using the same binding mode as other VPS29 effectors (e.g., RidL, TBC1D5, VARP). This interaction is distinct from VPS35:FAM21 contacts. The Parkinson's disease-linked VPS35 D620N mutation does not significantly impair direct FAM21 association in vitro.\",\n      \"method\": \"Crystal structure of VPS29:FAM21 peptide complex, in vitro binding assays, mutagenesis\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with in vitro binding validation; single lab but rigorous structural method\",\n      \"pmids\": [\"38607248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A third VPS29 isoform (VPS29C) harbors an extended N-terminal sequence that constitutes an autoinhibitory domain blocking the hydrophobic groove required for effector recruitment to Retromer and for association with Retriever and Commander complexes. VPS29C is therefore uniquely able to uncouple Retromer-dependent cargo sorting from broader VPS29A/B roles in accessory protein recruitment.\",\n      \"method\": \"AlphaFold structural modeling, in vitro complex reconstitution, mass spectrometry, molecular cell biology\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro reconstitution plus mass spectrometry plus cell biology; single lab; novel isoform identification with functional characterization\",\n      \"pmids\": [\"40587794\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In C. elegans, loss of vps-29 (cargo-selective retromer subunit) disrupts Wls recycling from endosomes to TGN, impairing Wnt secretion; this defect can be rescued by blocking late endosomal maturation, which accumulates Wls in late endosomes where it can be retrieved via an SNX-BAR-dependent retromer pathway, demonstrating that the VPS29-containing cargo-selective subcomplex preferentially acts at an early endosomal station distinct from the SNX-BAR pathway.\",\n      \"method\": \"C. elegans genetics (vps-29 loss-of-function), Wnt secretion assay, pharmacological inhibition of endosomal maturation, fluorescence microscopy\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic KO with defined cargo-sorting phenotype and pharmacological epistasis; single lab with two complementary approaches\",\n      \"pmids\": [\"24056045\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VARP directly interacts with SNX27 PDZ domain via its N-terminus, and VARP is required to reconstitute an endosomal supercomplex containing SNX27, ESCPE-1, and Retromer (VPS26/VPS35/VPS29) on PI(3)P-enriched membranes in a fully reconstituted biochemical system; specific point mutations in VARP abolish the VARP:SNX27 interaction in vitro.\",\n      \"method\": \"Biochemical reconstitution with purified mammalian proteins, AlphaFold2 Multimer modeling, liposome tubulation assay, in vitro binding assays, mutagenesis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous in vitro reconstitution with mutagenesis but preprint, single lab; provides mechanistic insight into VPS29-containing supercomplex assembly on membranes\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ATG5 associates with retromer core components VPS26, VPS29, and VPS35; knockout of ATG5 or other genes essential for membrane atg8ylation impairs retromer-dependent sorting of GLUT1 to the plasma membrane, independently of canonical autophagy, revealing a noncanonical role for membrane atg8ylation in retromer assembly and function.\",\n      \"method\": \"Co-immunoprecipitation, ATG5/atg8ylation gene knockouts, GLUT1 trafficking assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and KO with defined trafficking phenotype, but preprint and single lab; mechanistic link between atg8ylation and VPS29/retromer function is preliminary\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"VPS29 is a structurally rigid, phosphoesterase-fold scaffold subunit of the retromer heterotrimer (VPS26/VPS35/VPS29) that stabilizes the VPS29-VPS35 core, recruits accessory proteins (TBC1D5, VARP, FAM21/WASH complex, SNX1) via a conserved hydrophobic surface, controls Rab7 activity and retromer localization in neurons, and thereby mediates endosome-to-Golgi/TGN retrograde retrieval of transmembrane cargo receptors; whether VPS29 has intrinsic phosphatase activity remains contested, but the consensus favors a non-enzymatic scaffolding function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VPS29 is a core subunit of the cargo-selective retromer heterotrimer (VPS26/VPS35/VPS29) that mediates endosome-to-Golgi/TGN retrograde retrieval of transmembrane cargo receptors, established originally in yeast where vps29 loss mislocalizes the vacuolar sorting receptor Vps10p [#0] and conserved across metazoa for recycling of cargoes such as Wls during Wnt secretion [#11]. Structurally, VPS29 adopts a phosphoesterase fold but functions as a rigid, metal-independent scaffold rather than an enzyme: despite coordinating divalent metals in a putative active site, it shows no robust phosphatase activity and behaves as a conformationally stable platform [#1, #3]. It binds VPS35 with high affinity to form a stable VPS29-VPS35 core that protects VPS35 from proteasomal degradation, acting as a biologically stable intermediate during retromer assembly [#1, #4]. A single conserved hydrophobic surface on VPS29, distinct from the VPS35-binding site, serves as a hub for mutually competitive recruitment of accessory effectors—the Rab7 GAP TBC1D5, VARP, and the WASH-complex subunit FAM21—all of which engage this pocket through a shared β-hairpin/insertion binding mode, as does the Legionella effector RidL, which hijacks the site to displace TBC1D5 and block retrograde trafficking [#5, #6, #9]. Through this effector hub VPS29 controls retromer localization and Rab7 activity in neurons, where its loss mislocalizes retromer and Rab7 and produces endolysosomal and synaptic defects suppressed by reducing Rab7 or boosting TBC1D5 [#7]. VPS29-dependent control of endosome morphology, acidity, and protease activity also modulates viral entry, with opposing effects on coronaviruses versus influenza A [#8]. An N-terminally extended VPS29C isoform autoinhibits the hydrophobic groove, uncoupling retromer cargo sorting from accessory recruitment and from association with Retriever/Commander complexes [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established that VPS29 is required for retrograde retrieval of cargo receptors from the endosome to the Golgi, defining its core cellular function.\",\n      \"evidence\": \"Yeast vps29 loss-of-function with subcellular fractionation and CPY secretion/Vps10p localization assays\",\n      \"pmids\": [\"9105038\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the molecular mechanism or the partner subunits in mammals\", \"No structural basis for cargo selection\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Resolved the VPS29 fold and assembly logic, showing it forms a high-affinity heterotrimer with VPS35/VPS26 and presents a distinct hydrophobic surface for sorting-nexin assembly, while lacking detectable enzymatic activity.\",\n      \"evidence\": \"X-ray crystallography, in vitro phosphatase assay, mutagenesis, and in vivo trafficking assays in mammalian and yeast systems\",\n      \"pmids\": [\"15965486\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether the metal site has any in vivo catalytic role\", \"Full effector repertoire of the hydrophobic surface unknown\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Tested the hypothesis that VPS29 is a metal-dependent phosphatase, reporting Zn-dependent dephosphorylation of a CI-M6PR tail peptide requiring the assembled heterotrimer.\",\n      \"evidence\": \"In vitro phosphatase assays with recombinant VPS26/VPS35/VPS29, active-site mutagenesis, ICP-MS metal analysis, chelation\",\n      \"pmids\": [\"16737443\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab and subsequently contradicted\", \"No in-cell demonstration of phosphatase activity on a physiological substrate\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved the enzymatic controversy by demonstrating VPS29 is a rigid, metal-independent scaffold with no detectable phosphatase activity, recasting its role as structural rather than catalytic.\",\n      \"evidence\": \"X-ray crystallography, NMR (RDC, chemical shift mapping), ITC, and in vitro phosphatase assays\",\n      \"pmids\": [\"21629666\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Low-affinity SNX1 interaction implies additional in vivo determinants not captured in vitro\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showed that VPS29 stabilizes VPS35 against proteasomal degradation, explaining how the VPS29-VPS35 core is the obligate stable intermediate of retromer assembly.\",\n      \"evidence\": \"siRNA knockdown, in vitro subcomplex reconstitution, proteasome inhibition, immunoblotting\",\n      \"pmids\": [\"25937119\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanism of differential subcomplex stability not structurally defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed that the VPS29 hydrophobic surface is an exploitable effector hub by showing the Legionella effector RidL competitively displaces TBC1D5 to subvert retrograde trafficking and aid bacterial replication.\",\n      \"evidence\": \"Crystal structure of RidL:VPS29, mutagenesis, co-IP, in vitro binding, intracellular replication assays\",\n      \"pmids\": [\"29146912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not establish the full set of endogenous effectors using this site\", \"Consequences for specific cargo cohorts not mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined VARP as a competitive effector that binds the same VPS29 site as TBC1D5 and showed VPS29 acts upstream of Rab7 to control retromer localization in neurons.\",\n      \"evidence\": \"NMR and X-ray structures of VPS29:VARP, mutagenesis, in vivo competition and trafficking assays (mammalian); Drosophila genetics, epistasis, electrophysiology, EM\",\n      \"pmids\": [\"33024112\", \"32286230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How effector competition is regulated spatially/temporally is unresolved\", \"Direct biochemical link between VPS29 and Rab7 nucleotide state not reconstituted\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected VPS29-dependent endosome regulation to host susceptibility, showing its loss alters endosome morphology, acidity, and protease activity with opposing effects on coronavirus versus influenza A entry.\",\n      \"evidence\": \"Genome-wide CRISPR screen, VPS29 KO validation, viral infection assays, endosome acidity and protease assays\",\n      \"pmids\": [\"35229640\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking retromer function to endosomal protease activity not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed FAM21/WASH engages the VPS29 hydrophobic pocket via the same conserved binding mode as other effectors, consolidating a unified model of effector recruitment, and that the PD-linked VPS35 D620N does not impair direct FAM21:VPS29 contact.\",\n      \"evidence\": \"Crystal structure of VPS29:FAM21 peptide complex, in vitro binding, mutagenesis\",\n      \"pmids\": [\"38607248\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Single lab\", \"Cellular consequence of disrupting the direct VPS29:FAM21 contact not tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Reconstituted a VPS29-containing endosomal supercomplex, showing VARP bridges SNX27/ESCPE-1 and retromer on PI(3)P membranes.\",\n      \"evidence\": \"Biochemical reconstitution with purified proteins, AlphaFold2 Multimer modeling, liposome tubulation, mutagenesis (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab\", \"In-cell relevance of the reconstituted supercomplex not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a VPS29C isoform whose N-terminal extension autoinhibits the effector groove, providing a mechanism to uncouple retromer cargo sorting from accessory recruitment and Retriever/Commander association.\",\n      \"evidence\": \"AlphaFold modeling, in vitro complex reconstitution, mass spectrometry, cell biology\",\n      \"pmids\": [\"40587794\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Physiological contexts where VPS29C is expressed and used not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How effector competition at the single VPS29 hydrophobic surface is regulated in space and time to coordinate distinct trafficking routes, and how VPS29 controls Rab7 nucleotide state mechanistically, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No reconstitution of VPS29-directed Rab7 GAP regulation\", \"No structural model of full effector switching on assembled retromer\", \"Isoform-specific physiology unmapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4, 5, 6, 9]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 3, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 8, 11, 12]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 7, 11]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 8, 11]}\n    ],\n    \"complexes\": [\n      \"retromer (VPS26/VPS35/VPS29)\",\n      \"WASH complex (via FAM21)\",\n      \"Retriever/Commander\",\n      \"SNX27/ESCPE-1/Retromer supercomplex\"\n    ],\n    \"partners\": [\n      \"VPS35\",\n      \"VPS26\",\n      \"TBC1D5\",\n      \"VARP\",\n      \"FAM21\",\n      \"SNX1\",\n      \"RidL\",\n      \"ATG5\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}