{"gene":"NRBF2","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2000,"finding":"NRBF2 was identified as an interaction partner of peroxisome proliferator-activated receptor alpha (PPARα) and several other nuclear receptors via yeast two-hybrid screening, and exhibits gene activation function when tethered to a heterologous DNA binding domain in both mammalian cells and yeast.","method":"Yeast two-hybrid screening; reporter gene (gene activation) assay","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid plus functional reporter assay, single lab, two complementary methods","pmids":["10786636"],"is_preprint":false},{"year":2014,"finding":"NRBF2 is a component of the Atg14L-Beclin 1-Vps34-Vps15 (PI3KC3 Complex I) and directly binds Atg14L through its MIT domain, enhancing Atg14L-linked Vps34 kinase activity and autophagy induction; NRBF2-deficient mice develop focal liver necrosis and ductular reaction accompanied by impaired Atg14L-linked Vps34 activity.","method":"Co-immunoprecipitation; in vitro kinase assay; MIT domain binding mapping; NRBF2 knockout mouse model with histopathology","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vitro kinase assay, domain mapping, and in vivo KO model with defined phenotype; replicated across multiple cell and mouse experiments in one study","pmids":["24849286"],"is_preprint":false},{"year":2014,"finding":"NRBF2 is a specific member of Vps34 Complex I (containing Vps34, Vps15, Beclin-1, Atg14L, but not UVRAG) and directly interacts with Vps15 via its WD40 domain; NRBF2 knockdown inhibits starvation-induced autophagosome formation (GFP-LC3 puncta, LC3-II) and increases p62 levels.","method":"Co-immunoprecipitation; direct binding assay (Vps15 domain mapping); GFP-LC3 puncta assay; LC3-II western blot; siRNA knockdown","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with domain mapping, multiple autophagy flux readouts, consistent with independent publication same year","pmids":["24785657"],"is_preprint":false},{"year":2014,"finding":"NRBF2 interacts with Beclin 1 via its N-terminus and with Atg14L, forming part of the Atg14L-containing Beclin 1-Vps34 complex; NRBF2 deficiency increases intracellular PI3P levels and diminishes Atg14L-Vps34/Vps15 interactions, suggesting NRBF2 modulates Vps34 activity by stabilizing protein-protein interactions within the complex.","method":"Co-immunoprecipitation from mouse liver/brain; siRNA knockdown; PI3P measurement; co-localization with isolation membrane markers; N-terminus binding mapping","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical methods (Co-IP, PI3P assay, co-localization), single lab; note: functional interpretation (suppression vs. activation of Vps34) conflicts with other studies","pmids":["25086043"],"is_preprint":false},{"year":2016,"finding":"NRBF2 is a tightly bound fifth subunit of PI3KC3-C1 that enhances VPS34 lipid kinase activity ~10-fold, homodimerizes, and drives dimerization of the larger PI3KC3-C1 complex; hydrogen-deuterium exchange MS and negative-stain EM map NRBF2 to the base of the V-shaped complex, interacting primarily with the N-termini of ATG14 and BECN1.","method":"Hydrogen-deuterium exchange mass spectrometry (HDX-MS); negative-stain electron microscopy; in vitro lipid kinase assay; biochemical reconstitution","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with kinase assay, structural methods (HDX-MS + EM), multiple orthogonal approaches in one study","pmids":["27385829"],"is_preprint":false},{"year":2016,"finding":"The yeast NRBF2 ortholog Atg38 binds the Vps30-Atg14 subcomplex via its N-terminal MIT domain, bridging the coiled-coil I regions of Atg14 and Vps30 at the base of complex I; the 2.2 Å crystal structure of the Atg38 C-terminal domain shows a mushroom-like asymmetric homodimer with a 4-helix cap and parallel coiled-coil stalk; one Atg38 homodimer engages a single complex I, whereas human NRBF2 homodimer can bridge two complex I assemblies.","method":"HDX-MS; X-ray crystallography (2.2 Å); electron microscopy; biochemical reconstitution","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure at 2.2 Å, HDX-MS, and EM; multiple orthogonal structural methods","pmids":["27630019"],"is_preprint":false},{"year":2017,"finding":"MTORC1 phosphorylates NRBF2 at S113 and S120; phosphorylated NRBF2 preferentially interacts with PIK3C3/PIK3R4, whereas dephosphorylated NRBF2 (upon starvation or MTORC1 inhibition) shifts binding preference to ATG14/BECN1, increasing autophagic PI3KC3 complex assembly, ULK1 complex association, and PI3K lipid kinase activity and autophagy flux.","method":"In vitro kinase assay; phospho-site mutagenesis; co-immunoprecipitation; autophagy flux assays (LC3-II, GFP-LC3 puncta); mTOR inhibitor treatment","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay with site-specific mutagenesis, reciprocal Co-IP, multiple autophagy readouts, single rigorous study with orthogonal methods","pmids":["28059666"],"is_preprint":false},{"year":2017,"finding":"NRBF2 interacts with APP in vivo; NRBF2 overexpression promotes autophagic degradation of APP C-terminal fragments (APP-CTFs) and reduces Aβ1-40 and Aβ1-42 levels in APP-overexpressing cells; NRBF2 knockout attenuates recruitment of APP and APP-CTFs into phagophores and their sorting into endosomal intralumenal vesicles, leading to accumulation in RAB5-positive early endosomes.","method":"Co-immunoprecipitation (NRBF2–APP); NRBF2 overexpression/knockout cell lines; Aβ ELISA; immunofluorescence co-localization with phagophore and endosome markers; autophagy inhibitor experiments","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, gain/loss-of-function, multiple readouts, single lab","pmids":["28980867"],"is_preprint":false},{"year":2019,"finding":"NRBF2 deletion in mice impairs hippocampal autophagy, alters long-term potentiation (LTP), and promotes amyloid-β accumulation; AAV-mediated NRBF2 overexpression in hippocampus rescues impaired autophagy and memory deficits in NRBF2-depleted mice and reduces β-amyloid in an AD mouse model, placing NRBF2 in the BECN1-PIK3C3 complex as a functional regulator of brain autophagy and Aβ homeostasis.","method":"NRBF2 knockout mouse; AAV-mediated overexpression; behavioral memory tests; LTP electrophysiology; autophagic flux assays; Aβ measurement","journal":"Molecular neurodegeneration","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mouse + rescue by AAV overexpression with electrophysiology, behavioral, and biochemical readouts; multiple orthogonal approaches","pmids":["31775806"],"is_preprint":false},{"year":2020,"finding":"NRBF2 is required for generation of GTP-bound (active) RAB7 by interacting with the RAB7 GEF complex CCZ1-MON1A and maintaining its GEF activity; specifically, NRBF2 regulates CCZ1-MON1A interaction with PIK3C3/VPS34 and CCZ1-associated PI3KC3 kinase activity, which are required for CCZ1-MON1A GEF activity; NRBF2 functions as a RAB7 effector required for autophagosome maturation.","method":"Co-immunoprecipitation; GEF activity assay (RAB7 nucleotide exchange); autophagosome maturation assays (LC3, LAMP1 co-localization); NRBF2 KO cells; domain deletion analysis","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, biochemical GEF activity assay, multiple maturation readouts, domain mapping, KO cell rescue; multiple orthogonal methods","pmids":["32543313"],"is_preprint":false},{"year":2020,"finding":"NRBF2 is required for apoptotic cell clearance (efferocytosis) in macrophages; this requires NRBF2's interaction with the MON1-CCZ1 complex to activate RAB7 GEF activity and promote phagosome-lysosome fusion; adoptive transfer of wild-type macrophages into nrbf2−/− mice alleviates DSS-induced colitis.","method":"NRBF2 knockout mouse (DSS colitis model); macrophage efferocytosis assay; co-immunoprecipitation; RAB7 activation assay; adoptive macrophage transfer","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mouse in vivo model, adoptive transfer rescue, Co-IP, biochemical GEF assay; multiple orthogonal methods","pmids":["32160108"],"is_preprint":false},{"year":2021,"finding":"The MIT domain of NRBF2 interacts with RAB7 and promotes autophagosome maturation after subarachnoid hemorrhage; loss of NRBF2 impairs autophagosome maturation and exacerbates ER stress-associated neuroinflammation, while NRBF2 overexpression is protective, and the effect is blocked by a RAB7 antagonist (CID1067700).","method":"AAV-mediated NRBF2 overexpression/siRNA KD in SAH mouse model; MIT domain deletion mapping; co-immunoprecipitation (NRBF2–RAB7); RAB7 antagonist pharmacology; western blot and immunofluorescence","journal":"Journal of neuroinflammation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping, Co-IP, pharmacological validation, in vivo model; single lab","pmids":["34530854"],"is_preprint":false},{"year":2022,"finding":"The MIT domain of NRBF2 directly interacts with the PB1 domain of P62/SQSTM1; this interaction increases autophagic P62 body formation and regulates autophagy in small cell lung cancer cells; NRBF2 expression is transcriptionally regulated by the transcription factor XRCC6.","method":"Co-immunoprecipitation; domain mapping (MIT–PB1 interaction); autophagy flux assays; XRCC6 ChIP/reporter assays","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP with domain mapping, autophagy readouts; single lab, limited mechanistic depth in abstract","pmids":["35712081"],"is_preprint":false},{"year":2025,"finding":"NRBF2 binds PIK3R4/VPS15 through a conserved site on its N-terminal MIT domain with moderate affinity; this binding is mutually exclusive with UVRAG-containing PI3KC3-C2 because the UVRAG C2 domain outcompetes NRBF2 for VPS15 binding; the crystal structure of the NRBF2 coiled-coil (CC) domain reveals a symmetric homodimer with multiple hydrophobic pairings; CC-domain mutations that render NRBF2 monomeric weaken VPS15 binding and only partially rescue autophagy, while forced dimerization or tetramerization further enhances pro-autophagic activity.","method":"Crystal structure of NRBF2 CC domain; ITC (affinity measurement); co-immunoprecipitation; CC domain mutagenesis; Gcn4 dimerization/tetramerization fusion rescue assay; autophagy flux assays in nrbf2 KO cells","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure, ITC quantitative binding, mutagenesis with functional rescue, multiple orthogonal methods in one study","pmids":["41162841"],"is_preprint":false}],"current_model":"NRBF2 is a pro-autophagic fifth subunit of the ATG14-BECN1-PIK3C3/VPS34-PIK3R4/VPS15 (PI3KC3 Complex I) that homodimerizes via its coiled-coil domain to strengthen binding to VPS15 through its MIT domain, thereby enhancing VPS34 lipid kinase activity ~10-fold and promoting autophagy initiation; MTORC1-mediated phosphorylation at S113/S120 acts as a molecular switch that redirects NRBF2 from the catalytic (VPS34/VPS15) arm to the ATG14/BECN1 arm upon starvation to activate autophagy; additionally, NRBF2 promotes autophagosome maturation by interacting with the CCZ1-MON1A GEF complex and RAB7 to generate active GTP-RAB7 for phagosome-lysosome fusion, and is required for macrophage efferocytosis to limit intestinal inflammation."},"narrative":{"mechanistic_narrative":"NRBF2 is a pro-autophagic regulatory subunit of the autophagy-initiating PI3KC3 Complex I, where it controls VPS34 lipid kinase output and downstream autophagosome formation [PMID:24849286, PMID:24785657, PMID:27385829]. It is a tightly bound fifth subunit of the ATG14L–BECN1–VPS34(PIK3C3)–VPS15(PIK3R4) complex, contacting ATG14L and BECN1 through their N-termini and binding VPS15 through a conserved site on its N-terminal MIT domain, and in this configuration enhances ATG14L-linked VPS34 lipid kinase activity roughly ten-fold to drive autophagy induction [PMID:24849286, PMID:24785657, PMID:27385829, PMID:41162841]. Structural and biochemical work establishes that NRBF2 homodimerizes via its coiled-coil domain and maps to the base of the V-shaped complex; coiled-coil mutations that render it monomeric weaken VPS15 binding and only partially rescue autophagy, whereas forced dimerization or tetramerization further potentiates pro-autophagic activity, and its VPS15 engagement is mutually exclusive with the UVRAG-containing PI3KC3-C2 complex [PMID:27385829, PMID:27630019, PMID:41162841]. MTORC1 phosphorylates NRBF2 at S113 and S120, and this phosphorylation acts as a switch: phosphorylated NRBF2 favors the PIK3C3/PIK3R4 catalytic arm, while dephosphorylation upon starvation shifts binding toward ATG14L/BECN1, increasing autophagic complex assembly, ULK1 association, and lipid kinase activity [PMID:28059666]. Beyond initiation, NRBF2 promotes autophagosome maturation by acting as a RAB7 effector that engages the CCZ1–MON1A GEF complex to generate active GTP-RAB7 for phagosome–lysosome fusion, a function required for macrophage efferocytosis that limits intestinal inflammation [PMID:32543313, PMID:32160108]. In the brain, NRBF2 loss impairs hippocampal autophagy and promotes amyloid-β accumulation, and its restoration rescues autophagy and memory deficits, linking it to Aβ homeostasis [PMID:28980867, PMID:31775806].","teleology":[{"year":2000,"claim":"Before any autophagy role was known, NRBF2 was first characterized as a nuclear-receptor-associated factor, establishing the protein's existence and a transcriptional-coactivator-like activity.","evidence":"Yeast two-hybrid screen against PPARα and reporter gene activation assay in mammalian cells and yeast","pmids":["10786636"],"confidence":"Medium","gaps":["Does not connect NRBF2 to autophagy or VPS34 signaling","Physiological relevance of nuclear-receptor binding not established","No structural or domain basis for the interaction defined"]},{"year":2014,"claim":"The central question of NRBF2's molecular function was answered by identifying it as a component of PI3KC3 Complex I that binds ATG14L, VPS15, and BECN1 and enhances VPS34 kinase activity to drive autophagy.","evidence":"Reciprocal Co-IP with domain mapping (MIT to ATG14L; WD40/N-terminus to VPS15/BECN1), in vitro kinase assays, GFP-LC3/LC3-II/p62 flux readouts, siRNA knockdown, and an NRBF2-knockout mouse with focal liver necrosis","pmids":["24849286","24785657","25086043"],"confidence":"High","gaps":["One study reported NRBF2 deficiency raises PI3P and interpreted NRBF2 as a suppressor, conflicting with kinase-enhancement findings","Specificity for ATG14L (Complex I) vs UVRAG complex not fully resolved at this stage","Mechanism by which complex assembly increases catalytic output unknown"]},{"year":2016,"claim":"Structural and reconstitution work resolved how NRBF2 acts on the complex, showing it is a homodimerizing fifth subunit that sits at the base of the V-shaped assembly and can bridge two complexes.","evidence":"HDX-MS, negative-stain EM, in vitro lipid kinase assays with reconstituted complex, and a 2.2 Å crystal structure of the yeast Atg38 C-terminal domain","pmids":["27385829","27630019"],"confidence":"High","gaps":["How dimerization mechanistically couples to ~10-fold kinase enhancement not fully defined","In-cell consequence of bridging two complex I assemblies unclear","Regulation of the dimerization state in vivo not addressed"]},{"year":2017,"claim":"The regulatory logic of NRBF2 was established by showing MTORC1 phosphorylation toggles its arm preference within the complex, converting a nutrient signal into autophagy activation.","evidence":"In vitro kinase assay with S113/S120 phospho-site mutagenesis, reciprocal Co-IP, and autophagy flux assays under mTOR inhibition/starvation","pmids":["28059666"],"confidence":"High","gaps":["Phosphatase responsible for dephosphorylation upon starvation not identified","Quantitative stoichiometry of the arm switch in vivo unknown","Whether other kinases modify NRBF2 not addressed"]},{"year":2020,"claim":"NRBF2's role was extended beyond initiation to autophagosome maturation by demonstrating it acts as a RAB7 effector that sustains the CCZ1-MON1A GEF, linking it to membrane fusion and efferocytosis.","evidence":"Co-IP, RAB7 nucleotide-exchange GEF assays, LC3/LAMP1 maturation readouts, domain deletion, KO cells, plus a DSS-colitis mouse with macrophage adoptive-transfer rescue","pmids":["32543313","32160108"],"confidence":"High","gaps":["How a single protein coordinates both initiation (VPS34) and maturation (RAB7) functions not integrated","Direct vs PI3KC3-dependent contribution to GEF activity not fully separated","Tissue-specific requirements beyond macrophages not mapped"]},{"year":2019,"claim":"Physiological significance in the nervous system was established by showing NRBF2 governs hippocampal autophagy and amyloid-β clearance, with restoration rescuing memory deficits.","evidence":"NRBF2-knockout and AAV-overexpression mice with LTP electrophysiology, behavioral memory tests, autophagy flux, and Aβ measurements; APP Co-IP and endosome/phagophore co-localization in cells","pmids":["31775806","28980867"],"confidence":"High","gaps":["Whether Aβ effect is solely autophagy-mediated or also via endosomal sorting unclear","Direct relevance to human Alzheimer disease not established by causative mutation","Contribution of initiation vs maturation function to Aβ clearance not separated"]},{"year":2025,"claim":"Quantitative structural work refined the engagement model, defining the MIT-VPS15 binding affinity, the symmetric coiled-coil homodimer, and the competitive exclusivity with UVRAG.","evidence":"Crystal structure of the NRBF2 coiled-coil domain, ITC affinity measurement, Co-IP competition, CC-domain mutagenesis, and Gcn4-driven forced dimerization/tetramerization rescue in KO cells","pmids":["41162841"],"confidence":"High","gaps":["Physiological trigger controlling NRBF2 oligomerization state unknown","How UVRAG vs NRBF2 occupancy is balanced in cells not resolved","Relationship between MTORC1 phosphorylation and oligomerization not integrated"]},{"year":null,"claim":"It remains unresolved how NRBF2's distinct activities — VPS34 kinase enhancement at initiation, MTORC1-controlled arm switching, RAB7-effector maturation, and oligomerization control — are temporally and spatially coordinated within a single autophagy program.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking initiation and maturation roles","Upstream signals selecting between functions undefined","No human disease-causing mutation reported in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,4,6,13]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4,9]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,6]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1,2,4,6,9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6]}],"complexes":["PI3KC3 Complex I (ATG14L-BECN1-VPS34-VPS15)","CCZ1-MON1A RAB7 GEF complex"],"partners":["ATG14L","BECN1","PIK3C3","PIK3R4","RAB7","CCZ1","MON1A","SQSTM1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96F24","full_name":"Nuclear receptor-binding factor 2","aliases":["Comodulator of PPAR and RXR"],"length_aa":287,"mass_kda":32.4,"function":"May modulate transcriptional activation by target nuclear receptors. Can act as transcriptional activator (in vitro) Involved in starvation-induced autophagy probably by its association with PI3K complex I (PI3KC3-C1). However, effects has been described variably. Involved in the induction of starvation-induced autophagy (PubMed:24785657). Stabilizes PI3KC3-C1 assembly and enhances ATG14-linked lipid kinase activity of PIK3C3 (By similarity). Proposed to negatively regulate basal and starvation-induced autophagy and to inhibit PIK3C3 activity by modulating interactions in PI3KC3-C1 (PubMed:25086043). May be involved in autophagosome biogenesis (PubMed:25086043). May play a role in neural progenitor cell survival during differentiation (By similarity)","subcellular_location":"Nucleus; Cytoplasm; Cytoplasmic vesicle; Cytoplasmic vesicle, autophagosome","url":"https://www.uniprot.org/uniprotkb/Q96F24/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NRBF2","classification":"Not Classified","n_dependent_lines":180,"n_total_lines":1208,"dependency_fraction":0.1490066225165563},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ATG14","stoichiometry":10.0},{"gene":"ATL3","stoichiometry":0.2},{"gene":"POLR1C","stoichiometry":0.2},{"gene":"RAB14","stoichiometry":0.2},{"gene":"SEC13","stoichiometry":0.2},{"gene":"SEC24D","stoichiometry":0.2},{"gene":"SPTLC1","stoichiometry":0.2},{"gene":"TAF12","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NRBF2","total_profiled":1310},"omim":[{"mim_id":"616477","title":"NUCLEAR RECEPTOR-BINDING FACTOR 2; NRBF2","url":"https://www.omim.org/entry/616477"},{"mim_id":"607308","title":"MAMMOGRAPHIC DENSITY","url":"https://www.omim.org/entry/607308"},{"mim_id":"604503","title":"JUMONJI DOMAIN-CONTAINING PROTEIN 1C; JMJD1C","url":"https://www.omim.org/entry/604503"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NRBF2"},"hgnc":{"alias_symbol":["DKFZp564C1664","FLJ30395","COPR1","COPR2"],"prev_symbol":[]},"alphafold":{"accession":"Q96F24","domains":[{"cath_id":"1.20.58.80","chopping":"8-95","consensus_level":"medium","plddt":95.3657,"start":8,"end":95}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96F24","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96F24-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96F24-F1-predicted_aligned_error_v6.png","plddt_mean":72.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NRBF2","jax_strain_url":"https://www.jax.org/strain/search?query=NRBF2"},"sequence":{"accession":"Q96F24","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96F24.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96F24/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96F24"}},"corpus_meta":[{"pmid":"24849286","id":"PMC_24849286","title":"NRBF2 regulates autophagy and prevents liver injury by modulating Atg14L-linked phosphatidylinositol-3 kinase III activity.","date":"2014","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/24849286","citation_count":116,"is_preprint":false},{"pmid":"32160108","id":"PMC_32160108","title":"PI3KC3 complex subunit NRBF2 is required for apoptotic cell clearance to restrict intestinal inflammation.","date":"2020","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/32160108","citation_count":76,"is_preprint":false},{"pmid":"28059666","id":"PMC_28059666","title":"MTORC1-mediated NRBF2 phosphorylation functions as a switch for the class III PtdIns3K and autophagy.","date":"2017","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/28059666","citation_count":75,"is_preprint":false},{"pmid":"31775806","id":"PMC_31775806","title":"Autophagy protein NRBF2 has reduced expression in Alzheimer's brains and modulates memory and amyloid-beta homeostasis in 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macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39447807","citation_count":2,"is_preprint":false},{"pmid":"40013119","id":"PMC_40013119","title":"NRBF2 plays a crucial role in the acquisition process of learning and memory, independent of the Vps34 complex.","date":"2025","source":"Frontiers in behavioral neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/40013119","citation_count":0,"is_preprint":false},{"pmid":"41162841","id":"PMC_41162841","title":"NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the MIT domain to promote autophagy.","date":"2025","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/41162841","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.31.685958","title":"Senescent astrocytic deposits drive cognitive decline by disrupting tripartite synapse in the aging brain","date":"2025-11-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.31.685958","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15224,"output_tokens":4181,"usd":0.054193,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11899,"output_tokens":3588,"usd":0.074597,"stage2_stop_reason":"end_turn"},"total_usd":0.12879,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"NRBF2 was identified as an interaction partner of peroxisome proliferator-activated receptor alpha (PPARα) and several other nuclear receptors via yeast two-hybrid screening, and exhibits gene activation function when tethered to a heterologous DNA binding domain in both mammalian cells and yeast.\",\n      \"method\": \"Yeast two-hybrid screening; reporter gene (gene activation) assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid plus functional reporter assay, single lab, two complementary methods\",\n      \"pmids\": [\"10786636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NRBF2 is a component of the Atg14L-Beclin 1-Vps34-Vps15 (PI3KC3 Complex I) and directly binds Atg14L through its MIT domain, enhancing Atg14L-linked Vps34 kinase activity and autophagy induction; NRBF2-deficient mice develop focal liver necrosis and ductular reaction accompanied by impaired Atg14L-linked Vps34 activity.\",\n      \"method\": \"Co-immunoprecipitation; in vitro kinase assay; MIT domain binding mapping; NRBF2 knockout mouse model with histopathology\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vitro kinase assay, domain mapping, and in vivo KO model with defined phenotype; replicated across multiple cell and mouse experiments in one study\",\n      \"pmids\": [\"24849286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NRBF2 is a specific member of Vps34 Complex I (containing Vps34, Vps15, Beclin-1, Atg14L, but not UVRAG) and directly interacts with Vps15 via its WD40 domain; NRBF2 knockdown inhibits starvation-induced autophagosome formation (GFP-LC3 puncta, LC3-II) and increases p62 levels.\",\n      \"method\": \"Co-immunoprecipitation; direct binding assay (Vps15 domain mapping); GFP-LC3 puncta assay; LC3-II western blot; siRNA knockdown\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with domain mapping, multiple autophagy flux readouts, consistent with independent publication same year\",\n      \"pmids\": [\"24785657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NRBF2 interacts with Beclin 1 via its N-terminus and with Atg14L, forming part of the Atg14L-containing Beclin 1-Vps34 complex; NRBF2 deficiency increases intracellular PI3P levels and diminishes Atg14L-Vps34/Vps15 interactions, suggesting NRBF2 modulates Vps34 activity by stabilizing protein-protein interactions within the complex.\",\n      \"method\": \"Co-immunoprecipitation from mouse liver/brain; siRNA knockdown; PI3P measurement; co-localization with isolation membrane markers; N-terminus binding mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical methods (Co-IP, PI3P assay, co-localization), single lab; note: functional interpretation (suppression vs. activation of Vps34) conflicts with other studies\",\n      \"pmids\": [\"25086043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NRBF2 is a tightly bound fifth subunit of PI3KC3-C1 that enhances VPS34 lipid kinase activity ~10-fold, homodimerizes, and drives dimerization of the larger PI3KC3-C1 complex; hydrogen-deuterium exchange MS and negative-stain EM map NRBF2 to the base of the V-shaped complex, interacting primarily with the N-termini of ATG14 and BECN1.\",\n      \"method\": \"Hydrogen-deuterium exchange mass spectrometry (HDX-MS); negative-stain electron microscopy; in vitro lipid kinase assay; biochemical reconstitution\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with kinase assay, structural methods (HDX-MS + EM), multiple orthogonal approaches in one study\",\n      \"pmids\": [\"27385829\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The yeast NRBF2 ortholog Atg38 binds the Vps30-Atg14 subcomplex via its N-terminal MIT domain, bridging the coiled-coil I regions of Atg14 and Vps30 at the base of complex I; the 2.2 Å crystal structure of the Atg38 C-terminal domain shows a mushroom-like asymmetric homodimer with a 4-helix cap and parallel coiled-coil stalk; one Atg38 homodimer engages a single complex I, whereas human NRBF2 homodimer can bridge two complex I assemblies.\",\n      \"method\": \"HDX-MS; X-ray crystallography (2.2 Å); electron microscopy; biochemical reconstitution\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure at 2.2 Å, HDX-MS, and EM; multiple orthogonal structural methods\",\n      \"pmids\": [\"27630019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MTORC1 phosphorylates NRBF2 at S113 and S120; phosphorylated NRBF2 preferentially interacts with PIK3C3/PIK3R4, whereas dephosphorylated NRBF2 (upon starvation or MTORC1 inhibition) shifts binding preference to ATG14/BECN1, increasing autophagic PI3KC3 complex assembly, ULK1 complex association, and PI3K lipid kinase activity and autophagy flux.\",\n      \"method\": \"In vitro kinase assay; phospho-site mutagenesis; co-immunoprecipitation; autophagy flux assays (LC3-II, GFP-LC3 puncta); mTOR inhibitor treatment\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay with site-specific mutagenesis, reciprocal Co-IP, multiple autophagy readouts, single rigorous study with orthogonal methods\",\n      \"pmids\": [\"28059666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NRBF2 interacts with APP in vivo; NRBF2 overexpression promotes autophagic degradation of APP C-terminal fragments (APP-CTFs) and reduces Aβ1-40 and Aβ1-42 levels in APP-overexpressing cells; NRBF2 knockout attenuates recruitment of APP and APP-CTFs into phagophores and their sorting into endosomal intralumenal vesicles, leading to accumulation in RAB5-positive early endosomes.\",\n      \"method\": \"Co-immunoprecipitation (NRBF2–APP); NRBF2 overexpression/knockout cell lines; Aβ ELISA; immunofluorescence co-localization with phagophore and endosome markers; autophagy inhibitor experiments\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, gain/loss-of-function, multiple readouts, single lab\",\n      \"pmids\": [\"28980867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NRBF2 deletion in mice impairs hippocampal autophagy, alters long-term potentiation (LTP), and promotes amyloid-β accumulation; AAV-mediated NRBF2 overexpression in hippocampus rescues impaired autophagy and memory deficits in NRBF2-depleted mice and reduces β-amyloid in an AD mouse model, placing NRBF2 in the BECN1-PIK3C3 complex as a functional regulator of brain autophagy and Aβ homeostasis.\",\n      \"method\": \"NRBF2 knockout mouse; AAV-mediated overexpression; behavioral memory tests; LTP electrophysiology; autophagic flux assays; Aβ measurement\",\n      \"journal\": \"Molecular neurodegeneration\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mouse + rescue by AAV overexpression with electrophysiology, behavioral, and biochemical readouts; multiple orthogonal approaches\",\n      \"pmids\": [\"31775806\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NRBF2 is required for generation of GTP-bound (active) RAB7 by interacting with the RAB7 GEF complex CCZ1-MON1A and maintaining its GEF activity; specifically, NRBF2 regulates CCZ1-MON1A interaction with PIK3C3/VPS34 and CCZ1-associated PI3KC3 kinase activity, which are required for CCZ1-MON1A GEF activity; NRBF2 functions as a RAB7 effector required for autophagosome maturation.\",\n      \"method\": \"Co-immunoprecipitation; GEF activity assay (RAB7 nucleotide exchange); autophagosome maturation assays (LC3, LAMP1 co-localization); NRBF2 KO cells; domain deletion analysis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, biochemical GEF activity assay, multiple maturation readouts, domain mapping, KO cell rescue; multiple orthogonal methods\",\n      \"pmids\": [\"32543313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NRBF2 is required for apoptotic cell clearance (efferocytosis) in macrophages; this requires NRBF2's interaction with the MON1-CCZ1 complex to activate RAB7 GEF activity and promote phagosome-lysosome fusion; adoptive transfer of wild-type macrophages into nrbf2−/− mice alleviates DSS-induced colitis.\",\n      \"method\": \"NRBF2 knockout mouse (DSS colitis model); macrophage efferocytosis assay; co-immunoprecipitation; RAB7 activation assay; adoptive macrophage transfer\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mouse in vivo model, adoptive transfer rescue, Co-IP, biochemical GEF assay; multiple orthogonal methods\",\n      \"pmids\": [\"32160108\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The MIT domain of NRBF2 interacts with RAB7 and promotes autophagosome maturation after subarachnoid hemorrhage; loss of NRBF2 impairs autophagosome maturation and exacerbates ER stress-associated neuroinflammation, while NRBF2 overexpression is protective, and the effect is blocked by a RAB7 antagonist (CID1067700).\",\n      \"method\": \"AAV-mediated NRBF2 overexpression/siRNA KD in SAH mouse model; MIT domain deletion mapping; co-immunoprecipitation (NRBF2–RAB7); RAB7 antagonist pharmacology; western blot and immunofluorescence\",\n      \"journal\": \"Journal of neuroinflammation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping, Co-IP, pharmacological validation, in vivo model; single lab\",\n      \"pmids\": [\"34530854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The MIT domain of NRBF2 directly interacts with the PB1 domain of P62/SQSTM1; this interaction increases autophagic P62 body formation and regulates autophagy in small cell lung cancer cells; NRBF2 expression is transcriptionally regulated by the transcription factor XRCC6.\",\n      \"method\": \"Co-immunoprecipitation; domain mapping (MIT–PB1 interaction); autophagy flux assays; XRCC6 ChIP/reporter assays\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP with domain mapping, autophagy readouts; single lab, limited mechanistic depth in abstract\",\n      \"pmids\": [\"35712081\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NRBF2 binds PIK3R4/VPS15 through a conserved site on its N-terminal MIT domain with moderate affinity; this binding is mutually exclusive with UVRAG-containing PI3KC3-C2 because the UVRAG C2 domain outcompetes NRBF2 for VPS15 binding; the crystal structure of the NRBF2 coiled-coil (CC) domain reveals a symmetric homodimer with multiple hydrophobic pairings; CC-domain mutations that render NRBF2 monomeric weaken VPS15 binding and only partially rescue autophagy, while forced dimerization or tetramerization further enhances pro-autophagic activity.\",\n      \"method\": \"Crystal structure of NRBF2 CC domain; ITC (affinity measurement); co-immunoprecipitation; CC domain mutagenesis; Gcn4 dimerization/tetramerization fusion rescue assay; autophagy flux assays in nrbf2 KO cells\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure, ITC quantitative binding, mutagenesis with functional rescue, multiple orthogonal methods in one study\",\n      \"pmids\": [\"41162841\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NRBF2 is a pro-autophagic fifth subunit of the ATG14-BECN1-PIK3C3/VPS34-PIK3R4/VPS15 (PI3KC3 Complex I) that homodimerizes via its coiled-coil domain to strengthen binding to VPS15 through its MIT domain, thereby enhancing VPS34 lipid kinase activity ~10-fold and promoting autophagy initiation; MTORC1-mediated phosphorylation at S113/S120 acts as a molecular switch that redirects NRBF2 from the catalytic (VPS34/VPS15) arm to the ATG14/BECN1 arm upon starvation to activate autophagy; additionally, NRBF2 promotes autophagosome maturation by interacting with the CCZ1-MON1A GEF complex and RAB7 to generate active GTP-RAB7 for phagosome-lysosome fusion, and is required for macrophage efferocytosis to limit intestinal inflammation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NRBF2 is a pro-autophagic regulatory subunit of the autophagy-initiating PI3KC3 Complex I, where it controls VPS34 lipid kinase output and downstream autophagosome formation [#1, #2, #4]. It is a tightly bound fifth subunit of the ATG14L–BECN1–VPS34(PIK3C3)–VPS15(PIK3R4) complex, contacting ATG14L and BECN1 through their N-termini and binding VPS15 through a conserved site on its N-terminal MIT domain, and in this configuration enhances ATG14L-linked VPS34 lipid kinase activity roughly ten-fold to drive autophagy induction [#1, #2, #4, #13]. Structural and biochemical work establishes that NRBF2 homodimerizes via its coiled-coil domain and maps to the base of the V-shaped complex; coiled-coil mutations that render it monomeric weaken VPS15 binding and only partially rescue autophagy, whereas forced dimerization or tetramerization further potentiates pro-autophagic activity, and its VPS15 engagement is mutually exclusive with the UVRAG-containing PI3KC3-C2 complex [#4, #5, #13]. MTORC1 phosphorylates NRBF2 at S113 and S120, and this phosphorylation acts as a switch: phosphorylated NRBF2 favors the PIK3C3/PIK3R4 catalytic arm, while dephosphorylation upon starvation shifts binding toward ATG14L/BECN1, increasing autophagic complex assembly, ULK1 association, and lipid kinase activity [#6]. Beyond initiation, NRBF2 promotes autophagosome maturation by acting as a RAB7 effector that engages the CCZ1–MON1A GEF complex to generate active GTP-RAB7 for phagosome–lysosome fusion, a function required for macrophage efferocytosis that limits intestinal inflammation [#9, #10]. In the brain, NRBF2 loss impairs hippocampal autophagy and promotes amyloid-β accumulation, and its restoration rescues autophagy and memory deficits, linking it to Aβ homeostasis [#7, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Before any autophagy role was known, NRBF2 was first characterized as a nuclear-receptor-associated factor, establishing the protein's existence and a transcriptional-coactivator-like activity.\",\n      \"evidence\": \"Yeast two-hybrid screen against PPARα and reporter gene activation assay in mammalian cells and yeast\",\n      \"pmids\": [\"10786636\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not connect NRBF2 to autophagy or VPS34 signaling\", \"Physiological relevance of nuclear-receptor binding not established\", \"No structural or domain basis for the interaction defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The central question of NRBF2's molecular function was answered by identifying it as a component of PI3KC3 Complex I that binds ATG14L, VPS15, and BECN1 and enhances VPS34 kinase activity to drive autophagy.\",\n      \"evidence\": \"Reciprocal Co-IP with domain mapping (MIT to ATG14L; WD40/N-terminus to VPS15/BECN1), in vitro kinase assays, GFP-LC3/LC3-II/p62 flux readouts, siRNA knockdown, and an NRBF2-knockout mouse with focal liver necrosis\",\n      \"pmids\": [\"24849286\", \"24785657\", \"25086043\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"One study reported NRBF2 deficiency raises PI3P and interpreted NRBF2 as a suppressor, conflicting with kinase-enhancement findings\", \"Specificity for ATG14L (Complex I) vs UVRAG complex not fully resolved at this stage\", \"Mechanism by which complex assembly increases catalytic output unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Structural and reconstitution work resolved how NRBF2 acts on the complex, showing it is a homodimerizing fifth subunit that sits at the base of the V-shaped assembly and can bridge two complexes.\",\n      \"evidence\": \"HDX-MS, negative-stain EM, in vitro lipid kinase assays with reconstituted complex, and a 2.2 Å crystal structure of the yeast Atg38 C-terminal domain\",\n      \"pmids\": [\"27385829\", \"27630019\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How dimerization mechanistically couples to ~10-fold kinase enhancement not fully defined\", \"In-cell consequence of bridging two complex I assemblies unclear\", \"Regulation of the dimerization state in vivo not addressed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The regulatory logic of NRBF2 was established by showing MTORC1 phosphorylation toggles its arm preference within the complex, converting a nutrient signal into autophagy activation.\",\n      \"evidence\": \"In vitro kinase assay with S113/S120 phospho-site mutagenesis, reciprocal Co-IP, and autophagy flux assays under mTOR inhibition/starvation\",\n      \"pmids\": [\"28059666\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phosphatase responsible for dephosphorylation upon starvation not identified\", \"Quantitative stoichiometry of the arm switch in vivo unknown\", \"Whether other kinases modify NRBF2 not addressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"NRBF2's role was extended beyond initiation to autophagosome maturation by demonstrating it acts as a RAB7 effector that sustains the CCZ1-MON1A GEF, linking it to membrane fusion and efferocytosis.\",\n      \"evidence\": \"Co-IP, RAB7 nucleotide-exchange GEF assays, LC3/LAMP1 maturation readouts, domain deletion, KO cells, plus a DSS-colitis mouse with macrophage adoptive-transfer rescue\",\n      \"pmids\": [\"32543313\", \"32160108\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single protein coordinates both initiation (VPS34) and maturation (RAB7) functions not integrated\", \"Direct vs PI3KC3-dependent contribution to GEF activity not fully separated\", \"Tissue-specific requirements beyond macrophages not mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Physiological significance in the nervous system was established by showing NRBF2 governs hippocampal autophagy and amyloid-β clearance, with restoration rescuing memory deficits.\",\n      \"evidence\": \"NRBF2-knockout and AAV-overexpression mice with LTP electrophysiology, behavioral memory tests, autophagy flux, and Aβ measurements; APP Co-IP and endosome/phagophore co-localization in cells\",\n      \"pmids\": [\"31775806\", \"28980867\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Aβ effect is solely autophagy-mediated or also via endosomal sorting unclear\", \"Direct relevance to human Alzheimer disease not established by causative mutation\", \"Contribution of initiation vs maturation function to Aβ clearance not separated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Quantitative structural work refined the engagement model, defining the MIT-VPS15 binding affinity, the symmetric coiled-coil homodimer, and the competitive exclusivity with UVRAG.\",\n      \"evidence\": \"Crystal structure of the NRBF2 coiled-coil domain, ITC affinity measurement, Co-IP competition, CC-domain mutagenesis, and Gcn4-driven forced dimerization/tetramerization rescue in KO cells\",\n      \"pmids\": [\"41162841\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger controlling NRBF2 oligomerization state unknown\", \"How UVRAG vs NRBF2 occupancy is balanced in cells not resolved\", \"Relationship between MTORC1 phosphorylation and oligomerization not integrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how NRBF2's distinct activities — VPS34 kinase enhancement at initiation, MTORC1-controlled arm switching, RAB7-effector maturation, and oligomerization control — are temporally and spatially coordinated within a single autophagy program.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking initiation and maturation roles\", \"Upstream signals selecting between functions undefined\", \"No human disease-causing mutation reported in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 4, 6, 13]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4, 9]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1, 2, 4, 6, 9]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"PI3KC3 Complex I (ATG14L-BECN1-VPS34-VPS15)\",\n      \"CCZ1-MON1A RAB7 GEF complex\"\n    ],\n    \"partners\": [\n      \"ATG14L\",\n      \"BECN1\",\n      \"PIK3C3\",\n      \"PIK3R4\",\n      \"RAB7\",\n      \"CCZ1\",\n      \"MON1A\",\n      \"SQSTM1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}