Affinage

NRBF2

Nuclear receptor-binding factor 2 · UniProt Q96F24

Length
287 aa
Mass
32.4 kDa
Annotated
2026-06-10
21 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2000 Medium

    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

    PMID:10786636

    Open questions at the time
    • 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
  2. 2014 High

    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

    PMID:24785657 PMID:24849286 PMID:25086043

    Open questions at the time
    • 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
  3. 2016 High

    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

    PMID:27385829 PMID:27630019

    Open questions at the time
    • 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
  4. 2017 High

    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

    PMID:28059666

    Open questions at the time
    • Phosphatase responsible for dephosphorylation upon starvation not identified
    • Quantitative stoichiometry of the arm switch in vivo unknown
    • Whether other kinases modify NRBF2 not addressed
  5. 2020 High

    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

    PMID:32160108 PMID:32543313

    Open questions at the time
    • 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
  6. 2019 High

    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

    PMID:28980867 PMID:31775806

    Open questions at the time
    • 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
  7. 2025 High

    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

    PMID:41162841

    Open questions at the time
    • 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

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 5 GO:0060090 molecular adaptor activity 3 GO:0140110 transcription regulator activity 1
Localization
GO:0005829 cytosol 2 GO:0005634 nucleus 1
Pathway
R-HSA-9612973 Autophagy 5 R-HSA-162582 Signal Transduction 1 R-HSA-168256 Immune System 1
Partners
ATG14LBECN1CCZ1MON1APIK3C3PIK3R4RAB7SQSTM1
Complex memberships
CCZ1-MON1A RAB7 GEF complexPI3KC3 Complex I (ATG14L-BECN1-VPS34-VPS15)

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 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. Yeast two-hybrid screening; reporter gene (gene activation) assay Biochimica et biophysica acta Medium 10786636
2014 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. Co-immunoprecipitation; in vitro kinase assay; MIT domain binding mapping; NRBF2 knockout mouse model with histopathology Nature communications High 24849286
2014 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. Co-immunoprecipitation; direct binding assay (Vps15 domain mapping); GFP-LC3 puncta assay; LC3-II western blot; siRNA knockdown The Biochemical journal High 24785657
2014 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. Co-immunoprecipitation from mouse liver/brain; siRNA knockdown; PI3P measurement; co-localization with isolation membrane markers; N-terminus binding mapping The Journal of biological chemistry Medium 25086043
2016 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. Hydrogen-deuterium exchange mass spectrometry (HDX-MS); negative-stain electron microscopy; in vitro lipid kinase assay; biochemical reconstitution Proceedings of the National Academy of Sciences of the United States of America High 27385829
2016 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. HDX-MS; X-ray crystallography (2.2 Å); electron microscopy; biochemical reconstitution Autophagy High 27630019
2017 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. In vitro kinase assay; phospho-site mutagenesis; co-immunoprecipitation; autophagy flux assays (LC3-II, GFP-LC3 puncta); mTOR inhibitor treatment Autophagy High 28059666
2017 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. Co-immunoprecipitation (NRBF2–APP); NRBF2 overexpression/knockout cell lines; Aβ ELISA; immunofluorescence co-localization with phagophore and endosome markers; autophagy inhibitor experiments Autophagy Medium 28980867
2019 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. NRBF2 knockout mouse; AAV-mediated overexpression; behavioral memory tests; LTP electrophysiology; autophagic flux assays; Aβ measurement Molecular neurodegeneration High 31775806
2020 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. Co-immunoprecipitation; GEF activity assay (RAB7 nucleotide exchange); autophagosome maturation assays (LC3, LAMP1 co-localization); NRBF2 KO cells; domain deletion analysis Autophagy High 32543313
2020 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. NRBF2 knockout mouse (DSS colitis model); macrophage efferocytosis assay; co-immunoprecipitation; RAB7 activation assay; adoptive macrophage transfer Autophagy High 32160108
2021 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). 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 of neuroinflammation Medium 34530854
2022 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. Co-immunoprecipitation; domain mapping (MIT–PB1 interaction); autophagy flux assays; XRCC6 ChIP/reporter assays iScience Medium 35712081
2025 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. 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 Autophagy High 41162841

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 NRBF2 regulates autophagy and prevents liver injury by modulating Atg14L-linked phosphatidylinositol-3 kinase III activity. Nature communications 116 24849286
2020 PI3KC3 complex subunit NRBF2 is required for apoptotic cell clearance to restrict intestinal inflammation. Autophagy 76 32160108
2017 MTORC1-mediated NRBF2 phosphorylation functions as a switch for the class III PtdIns3K and autophagy. Autophagy 75 28059666
2019 Autophagy protein NRBF2 has reduced expression in Alzheimer's brains and modulates memory and amyloid-beta homeostasis in mice. Molecular neurodegeneration 73 31775806
2016 Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy. Proceedings of the National Academy of Sciences of the United States of America 70 27385829
2014 NRBF2 regulates macroautophagy as a component of Vps34 Complex I. The Biochemical journal 67 24785657
2017 NRBF2 is involved in the autophagic degradation process of APP-CTFs in Alzheimer disease models. Autophagy 66 28980867
2014 Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels. The Journal of biological chemistry 60 25086043
2016 Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex. Autophagy 54 27630019
2020 NRBF2 is a RAB7 effector required for autophagosome maturation and mediates the association of APP-CTFs with active form of RAB7 for degradation. Autophagy 43 32543313
2021 Autophagy protein NRBF2 attenuates endoplasmic reticulum stress-associated neuroinflammation and oxidative stress via promoting autophagosome maturation by interacting with Rab7 after SAH. Journal of neuroinflammation 39 34530854
2015 Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression. American journal of human genetics 31 26073781
2000 Nuclear receptor binding factor-2 (NRBF-2), a possible gene activator protein interacting with nuclear hormone receptors. Biochimica et biophysica acta 27 10786636
2023 Cell type-specific NRBF2 orchestrates autophagic flux and adult hippocampal neurogenesis in chronic stress-induced depression. Cell discovery 25 37644025
2021 Class III phosphatidylinositol 3-kinase complex I subunit NRBF2/Atg38 - from cell and structural biology to health and disease. Autophagy 20 33459128
2022 NRBF2 regulates the chemoresistance of small cell lung cancer by interacting with the P62 protein in the autophagy process. iScience 13 35712081
2022 NRBF2-mediated autophagy contributes to metabolite replenishment and radioresistance in glioblastoma. Experimental & molecular medicine 13 36333468
2020 Nuclear receptor binding factor 2 (NRBF2) is required for learning and memory. Laboratory investigation; a journal of technical methods and pathology 11 32350405
2024 miR-221-5p_R-4 regulates internalized trehalose-induced autophagy by targeting NRBF2 in porcine granulosa cells. International journal of biological macromolecules 2 39447807
2025 NRBF2 plays a crucial role in the acquisition process of learning and memory, independent of the Vps34 complex. Frontiers in behavioral neuroscience 0 40013119
2025 NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the MIT domain to promote autophagy. Autophagy 0 41162841

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