{"gene":"GGA3","run_date":"2026-06-10T01:55:21","timeline":{"discoveries":[{"year":2007,"finding":"GGA3 is required for lysosomal degradation of BACE1; caspase-3 cleaves GGA3 during apoptosis/ischemia, reducing GGA3 levels and thereby stabilizing BACE1 post-translationally, leading to elevated BACE1 levels and beta-secretase activity. RNAi silencing of GGA3 elevated BACE1 and Abeta levels.","method":"RNAi knockdown, caspase-3 cleavage assays, mouse cerebral ischemia model, AD brain samples","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RNAi, in vivo model, human brain tissue), replicated across subsequent studies","pmids":["17553422"],"is_preprint":false},{"year":2004,"finding":"GGA3 localizes to both the TGN and early endosomes. RNAi of GGA3 causes accumulation of the cation-independent mannose 6-phosphate receptor (CI-MPR) and internalized EGF in enlarged early endosomes, impairing EGF degradation and EGFR sorting to late endosomes. The VHS and GAT domains of GGA3 bind ubiquitin and interact with TSG101, a component of the ubiquitin-dependent sorting machinery.","method":"RNAi knockdown, protein interaction assays (pulldown/co-IP), subcellular fractionation, fluorescence microscopy","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interaction assays plus RNAi with defined cellular phenotype, replicated by structural studies","pmids":["15039775"],"is_preprint":false},{"year":2003,"finding":"Crystal structure of the GAE domain of human GGA3 in complex with a peptide from accessory protein Rabaptin-5 (DFGPLV sequence) resolved at 2.2 Å; leucine and valine residues of the peptide engage two contiguous shallow hydrophobic depressions and the anchoring phenylalanine is buried in a deep pocket formed by conserved arginine residues, an alanine, and a proline.","method":"X-ray crystallography at 2.2 Å resolution","journal":"Nature structural biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure with detailed binding interface characterization","pmids":["12858162"],"is_preprint":false},{"year":2006,"finding":"PACS-1 links GGA3 to CK2, forming a multimeric complex required for CI-MPR sorting. PACS-1-bound CK2 phosphorylates GGA3, releasing GGA3 from CI-MPR and early endosomes; CK2 also phosphorylates PACS-1 Ser278 to promote PACS-1 binding to CI-MPR for TGN retrieval. This defines a CK2-activated phosphorylation cascade coordinating GGA3-mediated TGN export and PACS-1-mediated endosome-to-TGN retrieval of CI-MPR.","method":"Co-immunoprecipitation, in vitro kinase assays, RNAi, subcellular fractionation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, in vitro kinase assays, and RNAi with defined sorting phenotype in single focused study","pmids":["16977309"],"is_preprint":false},{"year":2005,"finding":"Crystal structure of human GGA3 C-GAT domain in complex with ubiquitin reveals that a hydrophobic patch on C-GAT helices α1 and α2 binds the hydrophobic Ile44 surface of ubiquitin. Two distinct orientations of ubiquitin Arg42 give rise to two different binding modes. A second hydrophobic binding site on C-GAT helices α2 and α3, opposite to the first, also binds ubiquitin weakly.","method":"X-ray crystallography, NMR, biochemical binding assays","journal":"Genes to cells","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus NMR and biochemical validation of ubiquitin-binding mechanism","pmids":["15966896"],"is_preprint":false},{"year":2010,"finding":"GGA3 regulates BACE1 levels via the ubiquitin sorting machinery rather than solely via VHS domain–DXXLL motif interaction. BACE1 is ubiquitinated at lysine 501 (monoubiquitinated and Lys-63-linked polyubiquitinated). A GGA3 mutant with reduced ubiquitin-binding ability (GGA3-L276A) failed to regulate BACE1 levels, whereas mutations abrogating VHS–DXXLL binding (GGA3-N91A or BACE1-L499A/L500A) did not prevent GGA3-mediated regulation of BACE1.","method":"Mutagenesis, RNAi rescue/overexpression, ubiquitination assays, Western blotting in H4 neuroglioma cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site/binding-site mutagenesis of both GGA3 and BACE1, ubiquitination site mapping, rescue experiments with multiple mutants","pmids":["20484053"],"is_preprint":false},{"year":2005,"finding":"EGF receptor activation induces transient phosphorylation of GGA3 on Ser368 in the hinge segment, dependent on constitutive phosphorylation of Ser372. Phosphorylation requires neither EGF receptor internalization nor GGA3 membrane association, and can be blocked by MEK and PI3K pathway inhibitors. Phosphomimic mutations (S368D/S372D) decrease GGA3 association with organellar membranes.","method":"Phosphorylation mapping, site-directed mutagenesis, kinase inhibitor treatment, hydrodynamic radius analysis, membrane fractionation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — mutagenesis of specific phosphosites plus inhibitor experiments and functional membrane-association readout in one rigorous study","pmids":["16135791"],"is_preprint":false},{"year":2006,"finding":"hVPS18, a RING-H2 ubiquitin ligase, monoubiquitylates GGA3 at lysine 258 in the GAT domain. Ubiquitin binding to the GAT domain is a prerequisite for GGA3 ubiquitylation by hVPS18. Once ubiquitylated, the GAT domain can no longer bind ubiquitin, indicating that hVPS18-mediated ubiquitylation negatively regulates GGA3's ubiquitin-binding ability.","method":"In vitro ubiquitylation assays, mutagenesis (K258 and ubiquitin mutations), binding assays","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of ubiquitylation, mutagenesis of ubiquitylation site, functional readout of ubiquitin-binding loss; single lab","pmids":["16996030"],"is_preprint":false},{"year":2011,"finding":"GGA3 interacts selectively with the Met/HGF receptor tyrosine kinase upon stimulation and sorts Met for recycling from a Rab4 endosomal subdomain in association with 'gyrating' clathrin. GGA3 loss abolishes Met recycling, redirects Met toward degradation, and attenuates ERK activation and cell migration. Met recycling requires GGA3 interaction with Arf6 and association with the Crk adaptor.","method":"Co-immunoprecipitation, RNAi knockdown, recycling assays, live imaging of clathrin, ERK activation assays, migration assays","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, RNAi with multiple defined phenotypes (recycling, ERK, migration), domain-interaction mapping across orthogonal methods","pmids":["21664574"],"is_preprint":false},{"year":2012,"finding":"GGA3 is depleted while BACE1 increases acutely (48 h) after traumatic brain injury (TBI) in mice. BACE1 levels are increased in GGA3 null mouse brains in vivo. GGA1, a GGA3 homolog, is a novel caspase-3 substrate also depleted at 48 h post-TBI; GGA1 silencing potentiates BACE1 elevation caused by GGA3 deletion in neurons, indicating synergistic regulation. In the subacute phase (7 d), efficient BACE1 disposal depends solely on GGA3, not GGA1.","method":"Mouse TBI model, GGA3 knockout mice, GGA1/GGA3 double knockdown in neurons, Western blotting","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo knockout, TBI model, and in vitro double knockdown with defined quantitative phenotype","pmids":["22836275"],"is_preprint":false},{"year":2014,"finding":"RNF11 contains acidic-cluster dileucine (Ac-LL) motifs recognized by GGA VHS domains, directing RNF11 sorting at the TGN and internalization from the plasma membrane. RNF11 recruits the E3 ligase Itch to drive ubiquitination of GGA3, with catalytically inactive RNF11 causing GGA3 hyperubiquitination. Itch regulates endogenous GGA3 stability; GGA3 levels increase in cells knocked down for Itch.","method":"Co-immunoprecipitation, ubiquitination assays, RNAi, domain mapping, confocal microscopy","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and ubiquitination assays with RNF11/Itch knockdown, single lab with orthogonal methods","pmids":["25195858"],"is_preprint":false},{"year":2015,"finding":"GGA3 directly interacts with the TrkA cytoplasmic tail through an internal DXXLL motif and mediates TrkA recycling to the plasma membrane in an Arf6-dependent manner. GGA3 depletion delays TrkA recycling, accelerates TrkA degradation, attenuates sustained NGF-induced Akt activation, and reduces cell survival.","method":"Co-immunoprecipitation, RNAi knockdown, recycling assays, Akt phosphorylation assays, cell survival assays","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding (co-IP with domain mapping), RNAi with multiple readouts, single lab","pmids":["26446845"],"is_preprint":false},{"year":2016,"finding":"GGA3 knockdown reduces cell surface and total levels of α2, α5, and β1 integrin subunits, promotes their lysosomal degradation, inhibits cell spreading, reduces focal adhesion number, and impairs cell migration. Integrin trafficking and maintenance depend on the integrity of GGA3's Arf-binding site. GGA3 depletion mislocalizes sorting nexin 17 (SNX17) to enlarged late endosomes, implicating GGA3 in SNX17-dependent integrin recycling.","method":"RNAi knockdown, flow cytometry (surface levels), confocal microscopy, migration assays, focal adhesion staining","journal":"Traffic","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi with multiple orthogonal readouts (surface levels, degradation, migration, focal adhesions), domain-mutant analysis, single lab","pmids":["26935970"],"is_preprint":false},{"year":2016,"finding":"GGA3 physically interacts with α2B-adrenergic receptor (α2B-AR) via the triple Arg motif in the third intracellular loop of the receptor and the acidic EDWE motif in the VHS domain of GGA3. GGA3 knockdown arrests newly synthesized α2B-AR in the TGN, inhibiting its cell surface export and attenuating α2B-AR-mediated ERK1/2 activation and cAMP inhibition. α2A-AR does not interact with GGA3 and is unaffected by GGA3 knockdown.","method":"Co-immunoprecipitation, domain mutagenesis, inducible surface expression system, RNAi knockdown, ERK/cAMP signaling assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain mapping, inducible trafficking assay, functional signaling readouts; single lab","pmids":["26811329"],"is_preprint":false},{"year":2019,"finding":"GGA3 mediates GDNF-dependent slow recycling of the RET51 receptor tyrosine kinase isoform to the plasma membrane. GRB2 associates with RET51 C-terminal sequences, facilitating recruitment of active ARF6 and GGA3 interaction. GGA3 or ARF6 depletion reduces RET51 recycling and accelerates RET51 degradation, attenuates AKT activation, and impairs RET51-dependent cell motility, migration, and invasion.","method":"Co-immunoprecipitation, RNAi knockdown, recycling assays, AKT phosphorylation assays, migration/invasion assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with pathway dissection, RNAi with multiple defined phenotypes; single lab","pmids":["31645646"],"is_preprint":false},{"year":2020,"finding":"GGA3 regulates recycling of the prostaglandin D2 receptor DP1 through a Rab4-dependent mechanism. GGA3 interacts endogenously with DP1 (co-IP confirmed), with the interaction promoted by agonist stimulation. GGA3 interacts with intracellular loop 2 and C-terminus of DP1 via its VHS domain. An ARF-binding-deficient GGA3 mutant (N194A) still supports DP1 recycling. GGA3 also interacts with L-PGDS (co-IP and in vitro with purified proteins), and both GGA3 and L-PGDS function interdependently in DP1 recycling. GGA3 knockdown inhibits ERK1/2 activation following DP1 stimulation.","method":"Co-immunoprecipitation (endogenous), pulldown with purified recombinant proteins, confocal microscopy, domain mutagenesis, RNAi, recycling assays, ERK signaling assays","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — endogenous co-IP, in vitro reconstitution of L-PGDS interaction, domain mutant, multiple functional readouts; single lab","pmids":["32334026"],"is_preprint":false},{"year":2003,"finding":"GGA3 exists as two splice variants (GGA3-S and GGA3-L). By immunofluorescence microscopy, GGA1 and GGA3 show slightly different localization patterns at both the TGN and peripheral region. Overexpression of the dominant-negative VHS-GAT domain of GGA1 or GGA3-L redistributes TGN-associated GGA1 to the cytoplasm but does not affect GGA3 distribution.","method":"Western blotting, double immunofluorescence microscopy, dominant-negative overexpression","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single-lab localization study with overexpression dominant-negative; no functional rescue or binding partner validation","pmids":["12810073"],"is_preprint":false},{"year":2020,"finding":"GGA3 loss of function (genetic deletion or a rare AD-associated variant) disrupts axonal trafficking of BACE1, causing its accumulation in axonal swellings in cultured neurons and in vivo. Pharmacological BACE1 inhibition ameliorates axonal trafficking and reduces axonal dystrophies in Gga3-null neurons in vitro and in vivo. GGA3 deletion exacerbates axonal dystrophies in a mouse AD model before Aβ deposition.","method":"GGA3 knockout mice, primary neuron culture, BACE1 pharmacological inhibition, in vivo imaging/histology","journal":"Science translational medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo knockout and pharmacological rescue with defined axonal trafficking phenotype, replicated in vitro and in vivo","pmids":["33208500"],"is_preprint":false},{"year":2016,"finding":"GGA3 deletion in mice results in increased phasic GABAergic inhibition and decreased tonic inhibition in dentate gyrus granule cells, along with increased number of inhibitory synapses in the dentate gyrus, indicating a role for GGA3 in regulating GABAergic synaptic transmission.","method":"Electrophysiological recordings in hippocampal slices from GGA3 null mice, immunohistochemistry for inhibitory synapses","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo knockout with electrophysiology and morphological readouts, single lab, mechanism of GABAergic effect not fully elucidated","pmids":["27192432"],"is_preprint":false}],"current_model":"GGA3 is a multidomain clathrin adaptor that operates at the TGN, early endosomes, and recycling endosomes to sort transmembrane cargo: it traffics BACE1, CI-MPR, Met, TrkA, RET51, α2B-AR, DP1, and integrins by recognizing DXXLL motifs via its VHS domain and ubiquitinated cargo via its GAT domain (whose ubiquitin-binding activity is negatively regulated by hVPS18-mediated monoubiquitylation at K258 and by CK2/PACS-1-mediated phosphorylation); caspase-3 cleavage of GGA3 during apoptosis or injury depletes it, stabilizing BACE1 post-translationally and elevating amyloidogenic APP processing, while GGA3's recycling function—dependent on Arf6 and specific cargo interactions—sustains RTK-mediated ERK and Akt signaling, cell migration, and GABAergic synaptic transmission."},"narrative":{"mechanistic_narrative":"GGA3 is a multidomain clathrin adaptor that sorts transmembrane cargo at the trans-Golgi network (TGN) and endosomes by recognizing both acidic-cluster dileucine (DXXLL) motifs through its VHS domain and ubiquitinated cargo through its GAT domain [PMID:15039775, PMID:20484053]. Structural work defined how the GAT domain engages the Ile44 hydrophobic surface of ubiquitin in two distinct binding modes [PMID:15966896] and how the GAE domain captures accessory-protein peptides such as Rabaptin-5 via a hydrophobic interface [PMID:12858162]. Through these activities GGA3 controls sorting of CI-MPR, where it acts in a CK2/PACS-1 phosphorylation cascade that coordinates GGA3-mediated TGN export with PACS-1-mediated endosome-to-TGN retrieval [PMID:15039775, PMID:16977309]. Its cargo-sorting capacity is itself regulated by post-translational modification: hVPS18 monoubiquitylates the GAT domain at K258 to abolish its ubiquitin binding [PMID:16996030], EGFR-activated phosphorylation at Ser368/Ser372 in the hinge reduces membrane association [PMID:16135791], and the RNF11/Itch system controls GGA3 stability via ubiquitination [PMID:25195858]. A central role in disease is its control of BACE1: GGA3 directs BACE1 for lysosomal degradation via ubiquitin-dependent sorting (BACE1 ubiquitinated at K501), and caspase-3 cleavage of GGA3 during apoptosis, ischemia, or traumatic brain injury depletes it, stabilizing BACE1 and elevating amyloidogenic processing [PMID:17553422, PMID:20484053, PMID:22836275]; GGA3 loss also disrupts axonal BACE1 trafficking, and a rare AD-associated GGA3 variant produces axonal dystrophies rescued by BACE1 inhibition [PMID:33208500]. Beyond degradative sorting, GGA3 mediates Arf6-dependent recycling of receptor tyrosine kinases and GPCRs—Met, TrkA, RET51, the α2B-adrenergic receptor, and the prostaglandin DP1 receptor—sustaining ERK and Akt signaling, cell migration and invasion [PMID:21664574, PMID:26446845, PMID:26811329, PMID:31645646, PMID:32334026], and supports integrin recycling and cell spreading [PMID:26935970]. GGA3 deletion in mice additionally alters GABAergic synaptic transmission in the dentate gyrus [PMID:27192432].","teleology":[{"year":2003,"claim":"Resolving how GGA3 recruits accessory machinery established the structural basis for adaptor-coat assembly at the TGN.","evidence":"X-ray crystallography of the GGA3 GAE domain bound to a Rabaptin-5 peptide","pmids":["12858162"],"confidence":"High","gaps":["Does not address cargo recognition by VHS/GAT","Single peptide ligand; physiological stoichiometry in cells unaddressed"]},{"year":2003,"claim":"Identification of GGA3 splice variants and distinct sub-localization relative to GGA1 raised the question of functional specialization among GGA paralogs.","evidence":"Western blotting, double immunofluorescence, and dominant-negative VHS-GAT overexpression","pmids":["12810073"],"confidence":"Low","gaps":["Localization study by overexpression without functional rescue or partner validation","Functional distinction between GGA3-S and GGA3-L not established"]},{"year":2004,"claim":"Showing GGA3 binds ubiquitin and TSG101 and is required for CI-MPR and EGFR endosomal sorting reframed GGA3 as part of the ubiquitin-dependent sorting machinery, not solely a DXXLL adaptor.","evidence":"RNAi with CI-MPR/EGF endosome phenotypes, pulldown/co-IP, fractionation, microscopy","pmids":["15039775"],"confidence":"High","gaps":["Structural basis of ubiquitin binding not yet defined","Cargo ubiquitination sites unmapped"]},{"year":2005,"claim":"Crystallographic and NMR dissection of the GAT-ubiquitin interface defined the molecular mechanism by which GGA3 reads ubiquitinated cargo.","evidence":"X-ray crystallography, NMR, and biochemical binding assays of C-GAT with ubiquitin","pmids":["15966896"],"confidence":"High","gaps":["Physiological relevance of the second weak binding site unclear","Does not address regulation of binding in cells"]},{"year":2005,"claim":"Mapping EGFR-activated phosphorylation of GGA3 at Ser368/Ser372 linked receptor signaling to control of GGA3 membrane association.","evidence":"Phosphosite mapping, mutagenesis, MEK/PI3K inhibitors, membrane fractionation","pmids":["16135791"],"confidence":"High","gaps":["Kinase directly phosphorylating Ser368 not identified","Downstream cargo-sorting consequence not directly measured"]},{"year":2006,"claim":"Defining the CK2/PACS-1 cascade explained how GGA3 release from CI-MPR is coordinated with retrograde retrieval, establishing reciprocal phospho-regulation of bidirectional sorting.","evidence":"Co-IP, in vitro kinase assays, RNAi with CI-MPR sorting phenotype","pmids":["16977309"],"confidence":"High","gaps":["Phosphosites on GGA3 targeted by CK2 not fully mapped here","Generality to other GGA3 cargo not tested"]},{"year":2006,"claim":"Showing hVPS18 monoubiquitylates GGA3 at K258 to abolish GAT ubiquitin binding revealed a negative-feedback switch on GGA3's cargo-reading activity.","evidence":"In vitro ubiquitylation reconstitution, K258 mutagenesis, ubiquitin-binding assays","pmids":["16996030"],"confidence":"High","gaps":["In vitro reconstitution; cellular consequence on cargo flux not demonstrated","Deubiquitylation/reversal mechanism unknown"]},{"year":2007,"claim":"Demonstrating that caspase-3 cleavage of GGA3 stabilizes BACE1 connected GGA3 depletion to elevated beta-secretase activity, providing a mechanistic link to amyloidogenesis.","evidence":"RNAi, caspase-3 cleavage assays, mouse cerebral ischemia model, AD brain samples","pmids":["17553422"],"confidence":"High","gaps":["Whether sorting is via DXXLL or ubiquitin route not resolved here","Contribution of other GGAs not addressed"]},{"year":2010,"claim":"Mutational dissection established that GGA3 controls BACE1 chiefly through ubiquitin binding (GAT) rather than VHS-DXXLL recognition, refining the sorting mechanism.","evidence":"GGA3-L276A and N91A mutants, BACE1 K501 ubiquitination mapping, RNAi rescue in H4 cells","pmids":["20484053"],"confidence":"High","gaps":["E3 ligase ubiquitinating BACE1 not identified","Endosomal step where sorting occurs not pinpointed"]},{"year":2011,"claim":"Discovery that GGA3 sorts Met for recycling rather than degradation extended its role from degradative sorting to promotion of receptor signaling and migration.","evidence":"Co-IP, RNAi recycling/ERK/migration assays, live clathrin imaging, Arf6 and Crk interaction mapping","pmids":["21664574"],"confidence":"High","gaps":["How GGA3 switches cargo between recycling and degradation unclear","Role of gyrating clathrin mechanistically undefined"]},{"year":2012,"claim":"In vivo TBI and knockout studies showed GGA3 and its paralog GGA1 synergistically govern BACE1 disposal, with GGA3 dominant in the subacute phase.","evidence":"Mouse TBI model, GGA3 knockout, GGA1/GGA3 double knockdown in neurons","pmids":["22836275"],"confidence":"High","gaps":["Temporal switch from GGA1/GGA3 redundancy to GGA3 dependence not mechanistically explained"]},{"year":2014,"claim":"Identifying RNF11 as a GGA-sorted cargo that recruits Itch to ubiquitinate GGA3 revealed a feedback loop controlling GGA3 stability.","evidence":"Co-IP, ubiquitination assays, RNAi, domain mapping, confocal microscopy","pmids":["25195858"],"confidence":"Medium","gaps":["Single lab without reciprocal in vivo validation","Effect on GGA3-dependent cargo sorting not quantified"]},{"year":2015,"claim":"Showing GGA3 mediates Arf6-dependent TrkA recycling that sustains NGF-Akt signaling and survival generalized the recycling role to neurotrophin receptors.","evidence":"Co-IP with DXXLL domain mapping, RNAi recycling/Akt/survival assays","pmids":["26446845"],"confidence":"Medium","gaps":["Single lab","In vivo relevance to neuronal survival not established"]},{"year":2016,"claim":"Parallel studies established GGA3 as an Arf-dependent recycling adaptor for integrins, the α2B-adrenergic receptor, and as a regulator of GABAergic synaptic transmission, broadening its cargo repertoire.","evidence":"RNAi/flow cytometry/migration for integrins; co-IP, inducible export and signaling assays for α2B-AR; electrophysiology in GGA3-null hippocampal slices","pmids":["26935970","26811329","27192432"],"confidence":"Medium","gaps":["Cargo-specific recognition determinants vary (Arf-dependent vs Arf-independent) and are incompletely unified","Molecular basis of altered GABAergic transmission not identified"]},{"year":2019,"claim":"Demonstrating GGA3/ARF6-dependent recycling of RET51 downstream of GRB2 tied GGA3 to GDNF-driven AKT signaling and cancer cell invasion.","evidence":"Co-IP pathway dissection, RNAi recycling/AKT/invasion assays","pmids":["31645646"],"confidence":"Medium","gaps":["Single lab","Whether GGA3 selects RET51 over other RET isoforms mechanistically unresolved"]},{"year":2020,"claim":"GGA3 recycling activity was extended to a GPCR (DP1) via a Rab4/L-PGDS-dependent, Arf-independent route, and genetic studies linked GGA3 loss to disrupted axonal BACE1 trafficking and AD-relevant axonal dystrophies.","evidence":"Endogenous co-IP and in vitro reconstitution for DP1/L-PGDS; GGA3 knockout mice, AD-associated variant, and BACE1 inhibitor rescue for axonal phenotype","pmids":["32334026","33208500"],"confidence":"High","gaps":["How GGA3 selects Arf-dependent versus Arf-independent recycling routes is unclear","Penetrance and causality of the rare AD-associated GGA3 variant in human populations not established"]},{"year":null,"claim":"How GGA3 decides between degradative sorting and recycling for a given cargo, and how its multiple regulatory modifications are integrated in vivo, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of cargo fate determination","Interplay of K258 ubiquitylation, hinge phosphorylation, and Itch-mediated turnover not reconstituted together","E3 ligases acting on most GGA3 cargo undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,5,8,11,13,15]},{"term_id":"GO:0038024","term_label":"cargo receptor activity","supporting_discovery_ids":[1,5,12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,7]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1,3,13,16]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,3,8,15]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6,16]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,3,8,11,12]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[11,13,14,15]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[8,11,13,14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,9,17]}],"complexes":[],"partners":["BACE1","CI-MPR","TSG101","PACS-1","ARF6","MET","RET","RNF11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NZ52","full_name":"ADP-ribosylation factor-binding protein GGA3","aliases":["Golgi-localized, gamma ear-containing, ARF-binding protein 3"],"length_aa":723,"mass_kda":78.3,"function":"Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF-dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (DXXLL) motif (PubMed:11301005). Mediates export of the GPCR receptor ADRA2B to the cell surface (PubMed:26811329). nvolved in BACE1 transport and sorting as well as regulation of BACE1 protein levels (PubMed:15615712, PubMed:17553422, PubMed:20484053). Regulates retrograde transport of BACE1 from endosomes to the trans-Golgi network via interaction through the VHS motif and dependent of BACE1 phosphorylation (PubMed:15615712). Modulates BACE1 protein levels independently of the interaction between VHS domain and DXXLL motif through recognition of ubiquitination (PubMed:20484053). Key player in a novel DXXLL-mediated endosomal sorting machinery to the recycling pathway that targets NTRK1 to the plasma membrane (By similarity)","subcellular_location":"Golgi apparatus, trans-Golgi network membrane; Endosome membrane; Early endosome membrane; Recycling endosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9NZ52/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/GGA3","classification":"Not Classified","n_dependent_lines":29,"n_total_lines":1208,"dependency_fraction":0.024006622516556293},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/GGA3","total_profiled":1310},"omim":[{"mim_id":"617366","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 91; CCDC91","url":"https://www.omim.org/entry/617366"},{"mim_id":"606006","title":"GOLGI-ASSOCIATED, GAMMA-ADAPTIN EAR-CONTAINING, ARF-BINDING PROTEIN 3; GGA3","url":"https://www.omim.org/entry/606006"},{"mim_id":"606005","title":"GOLGI-ASSOCIATED, GAMMA-ADAPTIN EAR-CONTAINING, ARF-BINDING PROTEIN 2; GGA2","url":"https://www.omim.org/entry/606005"},{"mim_id":"606004","title":"GOLGI-ASSOCIATED, GAMMA-ADAPTIN EAR-CONTAINING, ARF-BINDING PROTEIN 1; GGA1","url":"https://www.omim.org/entry/606004"},{"mim_id":"604252","title":"BETA-SITE AMYLOID BETA A4 PRECURSOR PROTEIN-CLEAVING ENZYME 1; BACE1","url":"https://www.omim.org/entry/604252"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Golgi apparatus","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/GGA3"},"hgnc":{"alias_symbol":["KIAA0154"],"prev_symbol":[]},"alphafold":{"accession":"Q9NZ52","domains":[{"cath_id":"1.25.40.90","chopping":"10-142","consensus_level":"high","plddt":93.7911,"start":10,"end":142},{"cath_id":"1.20.5.170","chopping":"171-210","consensus_level":"medium","plddt":88.8618,"start":171,"end":210},{"cath_id":"1.20.58.160","chopping":"219-298","consensus_level":"medium","plddt":91.2643,"start":219,"end":298},{"cath_id":"2.60.40.1230","chopping":"589-720","consensus_level":"high","plddt":94.474,"start":589,"end":720}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZ52","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZ52-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZ52-F1-predicted_aligned_error_v6.png","plddt_mean":69.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=GGA3","jax_strain_url":"https://www.jax.org/strain/search?query=GGA3"},"sequence":{"accession":"Q9NZ52","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NZ52.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NZ52/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZ52"}},"corpus_meta":[{"pmid":"17553422","id":"PMC_17553422","title":"Depletion of GGA3 stabilizes BACE and enhances beta-secretase activity.","date":"2007","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/17553422","citation_count":292,"is_preprint":false},{"pmid":"15039775","id":"PMC_15039775","title":"Interactions of GGA3 with the ubiquitin sorting machinery.","date":"2004","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/15039775","citation_count":191,"is_preprint":false},{"pmid":"7846077","id":"PMC_7846077","title":"Specific 5'-GGGA-3'-->5'-GGA-3' mutation of the Apc gene in rat colon tumors induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.","date":"1995","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/7846077","citation_count":147,"is_preprint":false},{"pmid":"21664574","id":"PMC_21664574","title":"GGA3 functions as a switch to promote Met receptor recycling, essential for sustained ERK and cell migration.","date":"2011","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/21664574","citation_count":113,"is_preprint":false},{"pmid":"20484053","id":"PMC_20484053","title":"Ubiquitin regulates GGA3-mediated degradation of BACE1.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20484053","citation_count":87,"is_preprint":false},{"pmid":"16977309","id":"PMC_16977309","title":"A PACS-1, GGA3 and CK2 complex regulates CI-MPR trafficking.","date":"2006","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/16977309","citation_count":78,"is_preprint":false},{"pmid":"19815556","id":"PMC_19815556","title":"Down-regulation of seladin-1 increases BACE1 levels and activity through enhanced GGA3 depletion during apoptosis.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19815556","citation_count":59,"is_preprint":false},{"pmid":"22836275","id":"PMC_22836275","title":"Depletion of GGA1 and GGA3 mediates postinjury elevation of BACE1.","date":"2012","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/22836275","citation_count":54,"is_preprint":false},{"pmid":"12858162","id":"PMC_12858162","title":"Recognition of accessory protein motifs by the gamma-adaptin ear domain of GGA3.","date":"2003","source":"Nature structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/12858162","citation_count":50,"is_preprint":false},{"pmid":"26935970","id":"PMC_26935970","title":"Regulation of Cell Migration and β1 Integrin Trafficking by the Endosomal Adaptor GGA3.","date":"2016","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/26935970","citation_count":36,"is_preprint":false},{"pmid":"15966896","id":"PMC_15966896","title":"Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.","date":"2005","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/15966896","citation_count":36,"is_preprint":false},{"pmid":"21440067","id":"PMC_21440067","title":"Decreased expression of GGA3 protein in Alzheimer's disease frontal cortex and increased co-distribution of BACE with the amyloid precursor protein.","date":"2011","source":"Neurobiology of disease","url":"https://pubmed.ncbi.nlm.nih.gov/21440067","citation_count":32,"is_preprint":false},{"pmid":"17553417","id":"PMC_17553417","title":"Caspase-3 cleavage of GGA3 stabilizes BACE: implications for Alzheimer's disease.","date":"2007","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/17553417","citation_count":27,"is_preprint":false},{"pmid":"29391027","id":"PMC_29391027","title":"BACE1 elevation engendered by GGA3 deletion increases β-amyloid pathology in association with APP elevation and decreased CHL1 processing in 5XFAD mice.","date":"2018","source":"Molecular neurodegeneration","url":"https://pubmed.ncbi.nlm.nih.gov/29391027","citation_count":26,"is_preprint":false},{"pmid":"26811329","id":"PMC_26811329","title":"GGA3 Interacts with a G Protein-Coupled Receptor and Modulates Its Cell Surface Export.","date":"2016","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/26811329","citation_count":25,"is_preprint":false},{"pmid":"16996030","id":"PMC_16996030","title":"Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16996030","citation_count":24,"is_preprint":false},{"pmid":"16135791","id":"PMC_16135791","title":"Epidermal growth factor-dependent phosphorylation of the GGA3 adaptor protein regulates its recruitment to membranes.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16135791","citation_count":23,"is_preprint":false},{"pmid":"31645646","id":"PMC_31645646","title":"GGA3-mediated recycling of the RET receptor tyrosine kinase contributes to cell migration and invasion.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/31645646","citation_count":20,"is_preprint":false},{"pmid":"26446845","id":"PMC_26446845","title":"GGA3 mediates TrkA endocytic recycling to promote sustained Akt phosphorylation and cell survival.","date":"2015","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/26446845","citation_count":20,"is_preprint":false},{"pmid":"23970038","id":"PMC_23970038","title":"Elucidation of the BACE1 regulating factor GGA3 in Alzheimer's disease.","date":"2013","source":"Journal of Alzheimer's disease : JAD","url":"https://pubmed.ncbi.nlm.nih.gov/23970038","citation_count":19,"is_preprint":false},{"pmid":"12810073","id":"PMC_12810073","title":"Predominant expression of the short form of GGA3 in human cell lines and tissues.","date":"2003","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/12810073","citation_count":18,"is_preprint":false},{"pmid":"33208500","id":"PMC_33208500","title":"Gga3 deletion and a GGA3 rare variant associated with late onset Alzheimer's disease trigger BACE1 accumulation in axonal swellings.","date":"2020","source":"Science translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/33208500","citation_count":18,"is_preprint":false},{"pmid":"25195858","id":"PMC_25195858","title":"RNF11 is a GGA protein cargo and acts as a molecular adaptor for GGA3 ubiquitination mediated by Itch.","date":"2014","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/25195858","citation_count":18,"is_preprint":false},{"pmid":"35151205","id":"PMC_35151205","title":"Circ-GGA3 promotes the biological functions of human lens epithelial cells depending on the regulation of miR-497-5p/SMAD4 axis.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/35151205","citation_count":5,"is_preprint":false},{"pmid":"27192432","id":"PMC_27192432","title":"Genetic Deletion of the Clathrin Adaptor GGA3 Reduces Anxiety and Alters GABAergic Transmission.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27192432","citation_count":5,"is_preprint":false},{"pmid":"35117011","id":"PMC_35117011","title":"Up-regulated GGA3 promotes non-small cell lung cancer proliferation by regulating TrkA receptor.","date":"2019","source":"Translational cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/35117011","citation_count":2,"is_preprint":false},{"pmid":"32334026","id":"PMC_32334026","title":"GGA3 interacts with L-type prostaglandin D synthase and regulates the recycling and signaling of the DP1 receptor for prostaglandin D2 in a Rab4-dependent mechanism.","date":"2020","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/32334026","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14881,"output_tokens":5319,"usd":0.062214,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13583,"output_tokens":5109,"usd":0.09782,"stage2_stop_reason":"end_turn"},"total_usd":0.160034,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"GGA3 is required for lysosomal degradation of BACE1; caspase-3 cleaves GGA3 during apoptosis/ischemia, reducing GGA3 levels and thereby stabilizing BACE1 post-translationally, leading to elevated BACE1 levels and beta-secretase activity. RNAi silencing of GGA3 elevated BACE1 and Abeta levels.\",\n      \"method\": \"RNAi knockdown, caspase-3 cleavage assays, mouse cerebral ischemia model, AD brain samples\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RNAi, in vivo model, human brain tissue), replicated across subsequent studies\",\n      \"pmids\": [\"17553422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"GGA3 localizes to both the TGN and early endosomes. RNAi of GGA3 causes accumulation of the cation-independent mannose 6-phosphate receptor (CI-MPR) and internalized EGF in enlarged early endosomes, impairing EGF degradation and EGFR sorting to late endosomes. The VHS and GAT domains of GGA3 bind ubiquitin and interact with TSG101, a component of the ubiquitin-dependent sorting machinery.\",\n      \"method\": \"RNAi knockdown, protein interaction assays (pulldown/co-IP), subcellular fractionation, fluorescence microscopy\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interaction assays plus RNAi with defined cellular phenotype, replicated by structural studies\",\n      \"pmids\": [\"15039775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Crystal structure of the GAE domain of human GGA3 in complex with a peptide from accessory protein Rabaptin-5 (DFGPLV sequence) resolved at 2.2 Å; leucine and valine residues of the peptide engage two contiguous shallow hydrophobic depressions and the anchoring phenylalanine is buried in a deep pocket formed by conserved arginine residues, an alanine, and a proline.\",\n      \"method\": \"X-ray crystallography at 2.2 Å resolution\",\n      \"journal\": \"Nature structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure with detailed binding interface characterization\",\n      \"pmids\": [\"12858162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"PACS-1 links GGA3 to CK2, forming a multimeric complex required for CI-MPR sorting. PACS-1-bound CK2 phosphorylates GGA3, releasing GGA3 from CI-MPR and early endosomes; CK2 also phosphorylates PACS-1 Ser278 to promote PACS-1 binding to CI-MPR for TGN retrieval. This defines a CK2-activated phosphorylation cascade coordinating GGA3-mediated TGN export and PACS-1-mediated endosome-to-TGN retrieval of CI-MPR.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assays, RNAi, subcellular fractionation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, in vitro kinase assays, and RNAi with defined sorting phenotype in single focused study\",\n      \"pmids\": [\"16977309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Crystal structure of human GGA3 C-GAT domain in complex with ubiquitin reveals that a hydrophobic patch on C-GAT helices α1 and α2 binds the hydrophobic Ile44 surface of ubiquitin. Two distinct orientations of ubiquitin Arg42 give rise to two different binding modes. A second hydrophobic binding site on C-GAT helices α2 and α3, opposite to the first, also binds ubiquitin weakly.\",\n      \"method\": \"X-ray crystallography, NMR, biochemical binding assays\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus NMR and biochemical validation of ubiquitin-binding mechanism\",\n      \"pmids\": [\"15966896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"GGA3 regulates BACE1 levels via the ubiquitin sorting machinery rather than solely via VHS domain–DXXLL motif interaction. BACE1 is ubiquitinated at lysine 501 (monoubiquitinated and Lys-63-linked polyubiquitinated). A GGA3 mutant with reduced ubiquitin-binding ability (GGA3-L276A) failed to regulate BACE1 levels, whereas mutations abrogating VHS–DXXLL binding (GGA3-N91A or BACE1-L499A/L500A) did not prevent GGA3-mediated regulation of BACE1.\",\n      \"method\": \"Mutagenesis, RNAi rescue/overexpression, ubiquitination assays, Western blotting in H4 neuroglioma cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site/binding-site mutagenesis of both GGA3 and BACE1, ubiquitination site mapping, rescue experiments with multiple mutants\",\n      \"pmids\": [\"20484053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"EGF receptor activation induces transient phosphorylation of GGA3 on Ser368 in the hinge segment, dependent on constitutive phosphorylation of Ser372. Phosphorylation requires neither EGF receptor internalization nor GGA3 membrane association, and can be blocked by MEK and PI3K pathway inhibitors. Phosphomimic mutations (S368D/S372D) decrease GGA3 association with organellar membranes.\",\n      \"method\": \"Phosphorylation mapping, site-directed mutagenesis, kinase inhibitor treatment, hydrodynamic radius analysis, membrane fractionation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mutagenesis of specific phosphosites plus inhibitor experiments and functional membrane-association readout in one rigorous study\",\n      \"pmids\": [\"16135791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"hVPS18, a RING-H2 ubiquitin ligase, monoubiquitylates GGA3 at lysine 258 in the GAT domain. Ubiquitin binding to the GAT domain is a prerequisite for GGA3 ubiquitylation by hVPS18. Once ubiquitylated, the GAT domain can no longer bind ubiquitin, indicating that hVPS18-mediated ubiquitylation negatively regulates GGA3's ubiquitin-binding ability.\",\n      \"method\": \"In vitro ubiquitylation assays, mutagenesis (K258 and ubiquitin mutations), binding assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of ubiquitylation, mutagenesis of ubiquitylation site, functional readout of ubiquitin-binding loss; single lab\",\n      \"pmids\": [\"16996030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"GGA3 interacts selectively with the Met/HGF receptor tyrosine kinase upon stimulation and sorts Met for recycling from a Rab4 endosomal subdomain in association with 'gyrating' clathrin. GGA3 loss abolishes Met recycling, redirects Met toward degradation, and attenuates ERK activation and cell migration. Met recycling requires GGA3 interaction with Arf6 and association with the Crk adaptor.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, recycling assays, live imaging of clathrin, ERK activation assays, migration assays\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, RNAi with multiple defined phenotypes (recycling, ERK, migration), domain-interaction mapping across orthogonal methods\",\n      \"pmids\": [\"21664574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"GGA3 is depleted while BACE1 increases acutely (48 h) after traumatic brain injury (TBI) in mice. BACE1 levels are increased in GGA3 null mouse brains in vivo. GGA1, a GGA3 homolog, is a novel caspase-3 substrate also depleted at 48 h post-TBI; GGA1 silencing potentiates BACE1 elevation caused by GGA3 deletion in neurons, indicating synergistic regulation. In the subacute phase (7 d), efficient BACE1 disposal depends solely on GGA3, not GGA1.\",\n      \"method\": \"Mouse TBI model, GGA3 knockout mice, GGA1/GGA3 double knockdown in neurons, Western blotting\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo knockout, TBI model, and in vitro double knockdown with defined quantitative phenotype\",\n      \"pmids\": [\"22836275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RNF11 contains acidic-cluster dileucine (Ac-LL) motifs recognized by GGA VHS domains, directing RNF11 sorting at the TGN and internalization from the plasma membrane. RNF11 recruits the E3 ligase Itch to drive ubiquitination of GGA3, with catalytically inactive RNF11 causing GGA3 hyperubiquitination. Itch regulates endogenous GGA3 stability; GGA3 levels increase in cells knocked down for Itch.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, RNAi, domain mapping, confocal microscopy\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and ubiquitination assays with RNF11/Itch knockdown, single lab with orthogonal methods\",\n      \"pmids\": [\"25195858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"GGA3 directly interacts with the TrkA cytoplasmic tail through an internal DXXLL motif and mediates TrkA recycling to the plasma membrane in an Arf6-dependent manner. GGA3 depletion delays TrkA recycling, accelerates TrkA degradation, attenuates sustained NGF-induced Akt activation, and reduces cell survival.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, recycling assays, Akt phosphorylation assays, cell survival assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding (co-IP with domain mapping), RNAi with multiple readouts, single lab\",\n      \"pmids\": [\"26446845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"GGA3 knockdown reduces cell surface and total levels of α2, α5, and β1 integrin subunits, promotes their lysosomal degradation, inhibits cell spreading, reduces focal adhesion number, and impairs cell migration. Integrin trafficking and maintenance depend on the integrity of GGA3's Arf-binding site. GGA3 depletion mislocalizes sorting nexin 17 (SNX17) to enlarged late endosomes, implicating GGA3 in SNX17-dependent integrin recycling.\",\n      \"method\": \"RNAi knockdown, flow cytometry (surface levels), confocal microscopy, migration assays, focal adhesion staining\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi with multiple orthogonal readouts (surface levels, degradation, migration, focal adhesions), domain-mutant analysis, single lab\",\n      \"pmids\": [\"26935970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"GGA3 physically interacts with α2B-adrenergic receptor (α2B-AR) via the triple Arg motif in the third intracellular loop of the receptor and the acidic EDWE motif in the VHS domain of GGA3. GGA3 knockdown arrests newly synthesized α2B-AR in the TGN, inhibiting its cell surface export and attenuating α2B-AR-mediated ERK1/2 activation and cAMP inhibition. α2A-AR does not interact with GGA3 and is unaffected by GGA3 knockdown.\",\n      \"method\": \"Co-immunoprecipitation, domain mutagenesis, inducible surface expression system, RNAi knockdown, ERK/cAMP signaling assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain mapping, inducible trafficking assay, functional signaling readouts; single lab\",\n      \"pmids\": [\"26811329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"GGA3 mediates GDNF-dependent slow recycling of the RET51 receptor tyrosine kinase isoform to the plasma membrane. GRB2 associates with RET51 C-terminal sequences, facilitating recruitment of active ARF6 and GGA3 interaction. GGA3 or ARF6 depletion reduces RET51 recycling and accelerates RET51 degradation, attenuates AKT activation, and impairs RET51-dependent cell motility, migration, and invasion.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, recycling assays, AKT phosphorylation assays, migration/invasion assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with pathway dissection, RNAi with multiple defined phenotypes; single lab\",\n      \"pmids\": [\"31645646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"GGA3 regulates recycling of the prostaglandin D2 receptor DP1 through a Rab4-dependent mechanism. GGA3 interacts endogenously with DP1 (co-IP confirmed), with the interaction promoted by agonist stimulation. GGA3 interacts with intracellular loop 2 and C-terminus of DP1 via its VHS domain. An ARF-binding-deficient GGA3 mutant (N194A) still supports DP1 recycling. GGA3 also interacts with L-PGDS (co-IP and in vitro with purified proteins), and both GGA3 and L-PGDS function interdependently in DP1 recycling. GGA3 knockdown inhibits ERK1/2 activation following DP1 stimulation.\",\n      \"method\": \"Co-immunoprecipitation (endogenous), pulldown with purified recombinant proteins, confocal microscopy, domain mutagenesis, RNAi, recycling assays, ERK signaling assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — endogenous co-IP, in vitro reconstitution of L-PGDS interaction, domain mutant, multiple functional readouts; single lab\",\n      \"pmids\": [\"32334026\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"GGA3 exists as two splice variants (GGA3-S and GGA3-L). By immunofluorescence microscopy, GGA1 and GGA3 show slightly different localization patterns at both the TGN and peripheral region. Overexpression of the dominant-negative VHS-GAT domain of GGA1 or GGA3-L redistributes TGN-associated GGA1 to the cytoplasm but does not affect GGA3 distribution.\",\n      \"method\": \"Western blotting, double immunofluorescence microscopy, dominant-negative overexpression\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-lab localization study with overexpression dominant-negative; no functional rescue or binding partner validation\",\n      \"pmids\": [\"12810073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"GGA3 loss of function (genetic deletion or a rare AD-associated variant) disrupts axonal trafficking of BACE1, causing its accumulation in axonal swellings in cultured neurons and in vivo. Pharmacological BACE1 inhibition ameliorates axonal trafficking and reduces axonal dystrophies in Gga3-null neurons in vitro and in vivo. GGA3 deletion exacerbates axonal dystrophies in a mouse AD model before Aβ deposition.\",\n      \"method\": \"GGA3 knockout mice, primary neuron culture, BACE1 pharmacological inhibition, in vivo imaging/histology\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo knockout and pharmacological rescue with defined axonal trafficking phenotype, replicated in vitro and in vivo\",\n      \"pmids\": [\"33208500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"GGA3 deletion in mice results in increased phasic GABAergic inhibition and decreased tonic inhibition in dentate gyrus granule cells, along with increased number of inhibitory synapses in the dentate gyrus, indicating a role for GGA3 in regulating GABAergic synaptic transmission.\",\n      \"method\": \"Electrophysiological recordings in hippocampal slices from GGA3 null mice, immunohistochemistry for inhibitory synapses\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo knockout with electrophysiology and morphological readouts, single lab, mechanism of GABAergic effect not fully elucidated\",\n      \"pmids\": [\"27192432\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"GGA3 is a multidomain clathrin adaptor that operates at the TGN, early endosomes, and recycling endosomes to sort transmembrane cargo: it traffics BACE1, CI-MPR, Met, TrkA, RET51, α2B-AR, DP1, and integrins by recognizing DXXLL motifs via its VHS domain and ubiquitinated cargo via its GAT domain (whose ubiquitin-binding activity is negatively regulated by hVPS18-mediated monoubiquitylation at K258 and by CK2/PACS-1-mediated phosphorylation); caspase-3 cleavage of GGA3 during apoptosis or injury depletes it, stabilizing BACE1 post-translationally and elevating amyloidogenic APP processing, while GGA3's recycling function—dependent on Arf6 and specific cargo interactions—sustains RTK-mediated ERK and Akt signaling, cell migration, and GABAergic synaptic transmission.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"GGA3 is a multidomain clathrin adaptor that sorts transmembrane cargo at the trans-Golgi network (TGN) and endosomes by recognizing both acidic-cluster dileucine (DXXLL) motifs through its VHS domain and ubiquitinated cargo through its GAT domain [#1, #5]. Structural work defined how the GAT domain engages the Ile44 hydrophobic surface of ubiquitin in two distinct binding modes [#4] and how the GAE domain captures accessory-protein peptides such as Rabaptin-5 via a hydrophobic interface [#2]. Through these activities GGA3 controls sorting of CI-MPR, where it acts in a CK2/PACS-1 phosphorylation cascade that coordinates GGA3-mediated TGN export with PACS-1-mediated endosome-to-TGN retrieval [#1, #3]. Its cargo-sorting capacity is itself regulated by post-translational modification: hVPS18 monoubiquitylates the GAT domain at K258 to abolish its ubiquitin binding [#7], EGFR-activated phosphorylation at Ser368/Ser372 in the hinge reduces membrane association [#6], and the RNF11/Itch system controls GGA3 stability via ubiquitination [#10]. A central role in disease is its control of BACE1: GGA3 directs BACE1 for lysosomal degradation via ubiquitin-dependent sorting (BACE1 ubiquitinated at K501), and caspase-3 cleavage of GGA3 during apoptosis, ischemia, or traumatic brain injury depletes it, stabilizing BACE1 and elevating amyloidogenic processing [#0, #5, #9]; GGA3 loss also disrupts axonal BACE1 trafficking, and a rare AD-associated GGA3 variant produces axonal dystrophies rescued by BACE1 inhibition [#17]. Beyond degradative sorting, GGA3 mediates Arf6-dependent recycling of receptor tyrosine kinases and GPCRs—Met, TrkA, RET51, the \\u03b12B-adrenergic receptor, and the prostaglandin DP1 receptor—sustaining ERK and Akt signaling, cell migration and invasion [#8, #11, #13, #14, #15], and supports integrin recycling and cell spreading [#12]. GGA3 deletion in mice additionally alters GABAergic synaptic transmission in the dentate gyrus [#18].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Resolving how GGA3 recruits accessory machinery established the structural basis for adaptor-coat assembly at the TGN.\",\n      \"evidence\": \"X-ray crystallography of the GGA3 GAE domain bound to a Rabaptin-5 peptide\",\n      \"pmids\": [\"12858162\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address cargo recognition by VHS/GAT\", \"Single peptide ligand; physiological stoichiometry in cells unaddressed\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identification of GGA3 splice variants and distinct sub-localization relative to GGA1 raised the question of functional specialization among GGA paralogs.\",\n      \"evidence\": \"Western blotting, double immunofluorescence, and dominant-negative VHS-GAT overexpression\",\n      \"pmids\": [\"12810073\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Localization study by overexpression without functional rescue or partner validation\", \"Functional distinction between GGA3-S and GGA3-L not established\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showing GGA3 binds ubiquitin and TSG101 and is required for CI-MPR and EGFR endosomal sorting reframed GGA3 as part of the ubiquitin-dependent sorting machinery, not solely a DXXLL adaptor.\",\n      \"evidence\": \"RNAi with CI-MPR/EGF endosome phenotypes, pulldown/co-IP, fractionation, microscopy\",\n      \"pmids\": [\"15039775\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ubiquitin binding not yet defined\", \"Cargo ubiquitination sites unmapped\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Crystallographic and NMR dissection of the GAT-ubiquitin interface defined the molecular mechanism by which GGA3 reads ubiquitinated cargo.\",\n      \"evidence\": \"X-ray crystallography, NMR, and biochemical binding assays of C-GAT with ubiquitin\",\n      \"pmids\": [\"15966896\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological relevance of the second weak binding site unclear\", \"Does not address regulation of binding in cells\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapping EGFR-activated phosphorylation of GGA3 at Ser368/Ser372 linked receptor signaling to control of GGA3 membrane association.\",\n      \"evidence\": \"Phosphosite mapping, mutagenesis, MEK/PI3K inhibitors, membrane fractionation\",\n      \"pmids\": [\"16135791\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinase directly phosphorylating Ser368 not identified\", \"Downstream cargo-sorting consequence not directly measured\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defining the CK2/PACS-1 cascade explained how GGA3 release from CI-MPR is coordinated with retrograde retrieval, establishing reciprocal phospho-regulation of bidirectional sorting.\",\n      \"evidence\": \"Co-IP, in vitro kinase assays, RNAi with CI-MPR sorting phenotype\",\n      \"pmids\": [\"16977309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phosphosites on GGA3 targeted by CK2 not fully mapped here\", \"Generality to other GGA3 cargo not tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Showing hVPS18 monoubiquitylates GGA3 at K258 to abolish GAT ubiquitin binding revealed a negative-feedback switch on GGA3's cargo-reading activity.\",\n      \"evidence\": \"In vitro ubiquitylation reconstitution, K258 mutagenesis, ubiquitin-binding assays\",\n      \"pmids\": [\"16996030\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vitro reconstitution; cellular consequence on cargo flux not demonstrated\", \"Deubiquitylation/reversal mechanism unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrating that caspase-3 cleavage of GGA3 stabilizes BACE1 connected GGA3 depletion to elevated beta-secretase activity, providing a mechanistic link to amyloidogenesis.\",\n      \"evidence\": \"RNAi, caspase-3 cleavage assays, mouse cerebral ischemia model, AD brain samples\",\n      \"pmids\": [\"17553422\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether sorting is via DXXLL or ubiquitin route not resolved here\", \"Contribution of other GGAs not addressed\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Mutational dissection established that GGA3 controls BACE1 chiefly through ubiquitin binding (GAT) rather than VHS-DXXLL recognition, refining the sorting mechanism.\",\n      \"evidence\": \"GGA3-L276A and N91A mutants, BACE1 K501 ubiquitination mapping, RNAi rescue in H4 cells\",\n      \"pmids\": [\"20484053\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase ubiquitinating BACE1 not identified\", \"Endosomal step where sorting occurs not pinpointed\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Discovery that GGA3 sorts Met for recycling rather than degradation extended its role from degradative sorting to promotion of receptor signaling and migration.\",\n      \"evidence\": \"Co-IP, RNAi recycling/ERK/migration assays, live clathrin imaging, Arf6 and Crk interaction mapping\",\n      \"pmids\": [\"21664574\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How GGA3 switches cargo between recycling and degradation unclear\", \"Role of gyrating clathrin mechanistically undefined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"In vivo TBI and knockout studies showed GGA3 and its paralog GGA1 synergistically govern BACE1 disposal, with GGA3 dominant in the subacute phase.\",\n      \"evidence\": \"Mouse TBI model, GGA3 knockout, GGA1/GGA3 double knockdown in neurons\",\n      \"pmids\": [\"22836275\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Temporal switch from GGA1/GGA3 redundancy to GGA3 dependence not mechanistically explained\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying RNF11 as a GGA-sorted cargo that recruits Itch to ubiquitinate GGA3 revealed a feedback loop controlling GGA3 stability.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, RNAi, domain mapping, confocal microscopy\",\n      \"pmids\": [\"25195858\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab without reciprocal in vivo validation\", \"Effect on GGA3-dependent cargo sorting not quantified\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showing GGA3 mediates Arf6-dependent TrkA recycling that sustains NGF-Akt signaling and survival generalized the recycling role to neurotrophin receptors.\",\n      \"evidence\": \"Co-IP with DXXLL domain mapping, RNAi recycling/Akt/survival assays\",\n      \"pmids\": [\"26446845\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"In vivo relevance to neuronal survival not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Parallel studies established GGA3 as an Arf-dependent recycling adaptor for integrins, the \\u03b12B-adrenergic receptor, and as a regulator of GABAergic synaptic transmission, broadening its cargo repertoire.\",\n      \"evidence\": \"RNAi/flow cytometry/migration for integrins; co-IP, inducible export and signaling assays for \\u03b12B-AR; electrophysiology in GGA3-null hippocampal slices\",\n      \"pmids\": [\"26935970\", \"26811329\", \"27192432\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cargo-specific recognition determinants vary (Arf-dependent vs Arf-independent) and are incompletely unified\", \"Molecular basis of altered GABAergic transmission not identified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating GGA3/ARF6-dependent recycling of RET51 downstream of GRB2 tied GGA3 to GDNF-driven AKT signaling and cancer cell invasion.\",\n      \"evidence\": \"Co-IP pathway dissection, RNAi recycling/AKT/invasion assays\",\n      \"pmids\": [\"31645646\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Whether GGA3 selects RET51 over other RET isoforms mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"GGA3 recycling activity was extended to a GPCR (DP1) via a Rab4/L-PGDS-dependent, Arf-independent route, and genetic studies linked GGA3 loss to disrupted axonal BACE1 trafficking and AD-relevant axonal dystrophies.\",\n      \"evidence\": \"Endogenous co-IP and in vitro reconstitution for DP1/L-PGDS; GGA3 knockout mice, AD-associated variant, and BACE1 inhibitor rescue for axonal phenotype\",\n      \"pmids\": [\"32334026\", \"33208500\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How GGA3 selects Arf-dependent versus Arf-independent recycling routes is unclear\", \"Penetrance and causality of the rare AD-associated GGA3 variant in human populations not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How GGA3 decides between degradative sorting and recycling for a given cargo, and how its multiple regulatory modifications are integrated in vivo, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of cargo fate determination\", \"Interplay of K258 ubiquitylation, hinge phosphorylation, and Itch-mediated turnover not reconstituted together\", \"E3 ligases acting on most GGA3 cargo undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 5, 8, 11, 13, 15]},\n      {\"term_id\": \"GO:0038024\", \"supporting_discovery_ids\": [1, 5, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1, 3, 13, 16]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 3, 8, 15]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6, 16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 3, 8, 11, 12]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [11, 13, 14, 15]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [8, 11, 13, 14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 9, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"BACE1\", \"CI-MPR\", \"TSG101\", \"PACS-1\", \"Arf6\", \"MET\", \"RET\", \"RNF11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}