{"gene":"UBL4A","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2012,"finding":"SGTA contains a noncanonical ubiquitin-like-binding domain (UBD) that interacts specifically with the unconventional ubiquitin-like domain of Ubl4A, at least in part via electrostatics. This interaction recruits SGTA to the BAG6 complex, enhances substrate loading to BAG6, and prevents formation of nondegradable protein aggregates during ERAD.","method":"NMR spectroscopy, biochemical binding assays, co-immunoprecipitation","journal":"Cell Reports","confidence":"High","confidence_rationale":"Tier 1/2 / Strong — NMR structure determination combined with biochemical assays; replicated across multiple studies (PMIDs 23142665, 23297211, 25415308)","pmids":["23246001"],"is_preprint":false},{"year":2010,"finding":"Get4 (TRC35) and Get5 (UBL4A/Mdy2) form a tight complex in yeast, and Get3 specifically binds to a conserved surface on Get4 in a nucleotide-dependent manner, placing Get4/5 upstream of Get3 in the tail-anchored protein targeting pathway.","method":"Crystal structure of Get4/Get5 N-terminal fragment, co-immunoprecipitation, isothermal titration calorimetry","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus biochemical validation; independently replicated by Chang et al. (PMID 20106980)","pmids":["20554915","20106980"],"is_preprint":false},{"year":2012,"finding":"The N-terminal dimerization domain of Sgt2/SGTA directly binds the UBL domain of Get5/UBL4A via electrostatics, forming a high-affinity complex with rapid kinetics, structurally characterized for both yeast and human protein pairs.","method":"Crystal structures (yeast and human UBD/UBL complex), biophysical studies (ITC, NMR chemical shift perturbation)","journal":"Cell Reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures for both yeast and human proteins, multiple orthogonal biophysical methods, independently replicated (PMIDs 23246001, 23297211, 24100326, 25415308)","pmids":["23142665"],"is_preprint":false},{"year":2013,"finding":"Solution structure of Sgt2_NT (unique helical fold) and crystal structure of Get5_UBL determined; NMR chemical shift perturbation and ITC establish a 1:2 stoichiometry (one Get5 UBL to one Sgt2 dimer); site-directed mutagenesis validated the binding interface.","method":"NMR solution structure, crystal structure, isothermal titration calorimetry, site-directed mutagenesis, relaxation experiments","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal structural and biophysical methods with mutagenesis validation in a single rigorous study","pmids":["23297211"],"is_preprint":false},{"year":2014,"finding":"Crystal structure of yeast Get3-Get4-Get5 ternary complex in an ATP-bound state reveals that Get4 primes Get3 by promoting an optimal configuration for TA substrate capture; Get4-mediated regulation of Get3 ATP hydrolysis is essential for efficient TA-protein targeting.","method":"Crystal structure, structure-guided biochemical assays, ATPase activity measurements","journal":"Nature Structural & Molecular Biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of ternary complex combined with structure-guided mutagenesis and functional assays in a single high-rigor study","pmids":["24727835"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the C-terminal heterodimerization domains of BAG6 and Ubl4A reveals a novel binding interface; the BAG6 C-terminus (designated BAGS domain) is structurally distinct from canonical BAG domains. Tight association of BAG6 and Ubl4A modulates Ubl4A protein stability in cells.","method":"Crystal structure, biochemical binding assays, cell-based stability assays","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with biochemical and cell-based validation in a single study","pmids":["25713138"],"is_preprint":false},{"year":2014,"finding":"NMR solution structure of the SGTA dimerization domain determined; UBL domains from UBL4A and BAG6 compete for binding to SGTA at the same site, characterized by NMR chemical shift perturbation, ITC, and microscale thermophoresis; HADDOCK docking models of SGTA-UBL complexes generated.","method":"NMR structure determination, ITC, microscale thermophoresis, NMR chemical shift perturbation","journal":"PLoS ONE","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with three independent biophysical methods for interaction characterization","pmids":["25415308"],"is_preprint":false},{"year":2013,"finding":"Nuclear BAG6-UBL4A-GET4 complex mediates DNA damage signaling and cell death. Upon DNA damage, UBL4A and GET4 translocate to the nucleus. Depletion of BAG6 causes loss of both UBL4A and GET4 proteins. Co-depletion of UBL4A and GET4 (but not single depletion) confers resistance to DNA damage-induced cell death. All three components regulate BRCA1 recruitment to DNA damage sites.","method":"siRNA knockdown, cell viability assays, immunofluorescence for nuclear translocation, BRCA1 recruitment assays","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined cellular phenotype, multiple functional readouts, single lab","pmids":["23723067"],"is_preprint":false},{"year":2015,"finding":"Ubl4A directly interacts with the Arp2/3 complex to accelerate actin branching and networking, enabling insulin-induced Akt translocation to the plasma membrane. Ubl4A knockout mice have defective Akt-dependent glycogen synthesis. Akt binds actin filaments and colocalizes with Arp2/3 in membrane ruffles.","method":"Protein-protein interaction assays, actin branching in vitro assays, Ubl4A knockout mouse model, live-cell imaging of Akt translocation, glycogen synthesis assays","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1/2 / Strong — in vitro actin branching assay, direct interaction demonstrated, KO mouse with defined metabolic phenotype, multiple orthogonal methods","pmids":["26195787"],"is_preprint":false},{"year":2016,"finding":"Ubl4A, F-actin, and Arp2/3 co-localize at cell leading edges during wound closure. Knockout of Ubl4A reduces actin-mediated membrane protrusion, delays wound healing in primary mouse embryonic fibroblasts, impairs fibroblast migration from corneal tissue ex vivo, and decreases macrophage motility without affecting phagocytosis.","method":"Ubl4A KO mouse model, wound-healing assay, immunofluorescence co-localization, ex vivo migration assay, macrophage motility and phagocytosis assays","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse with specific cellular phenotype, multiple cell types and assays, single lab","pmids":["27998771"],"is_preprint":false},{"year":2018,"finding":"The C-terminal region of Ubl4A directly interacts with the Arp2/3 complex in pull-down assays. A point mutation D122A in the C-terminus abolishes Arp2/3 binding and destabilizes Ubl4A. Wild-type Ubl4A induces cell death in colon cancer cells via its C-terminal Arp2/3-binding activity, while D122A mutant loses this pro-death activity.","method":"In vitro protein pull-down, site-directed mutagenesis (D122A), cell death assays","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 1/2 / Weak — in vitro pull-down with mutagenesis, cell-based functional validation, single lab single study","pmids":["30146258"],"is_preprint":false},{"year":2019,"finding":"GdX/UBL4A positively regulates NF-κB signaling in dendritic cells and macrophages by trapping TC45 (PTPN2), thereby disrupting the TC45/PP2A/p65 complex that mediates p65 dephosphorylation and preventing p65 dephosphorylation.","method":"Immunoprecipitation, luciferase reporter assay, LPS challenge of GdX-deficient mice, cytokine ELISA, DSS colitis model with tissue-specific KO mice","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP, reporter assay, and in vivo KO models with defined immune phenotype; single lab","pmids":["30867837"],"is_preprint":false},{"year":2019,"finding":"UBL4A interacts with TRAF6 via co-immunoprecipitation, and this interaction is enhanced upon viral infection. UBL4A promotes K63-linked ubiquitination of TRAF6, enhancing TBK1, IRF3, and IKKα/β phosphorylation and type I IFN transcription.","method":"Co-immunoprecipitation, ubiquitination assay (K63-specific), siRNA knockdown and overexpression, phosphorylation western blots","journal":"Journal of Immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus K63-specific ubiquitination assay and functional phosphorylation readouts; single lab","pmids":["31451677"],"is_preprint":false},{"year":2019,"finding":"UBL4A directly interacts with LAMP1 by co-immunoprecipitation and causes lysosomal dysfunction leading to impaired autophagic degradation and autophagosome accumulation in pancreatic cancer cells. LAMP1 overexpression reverses the antitumor effects of UBL4A.","method":"Co-immunoprecipitation, western blot autophagy markers, in vitro and in vivo (orthotopic) functional assays","journal":"Journal of Experimental & Clinical Cancer Research","confidence":"Medium","confidence_rationale":"Tier 2/3 / Moderate — co-IP with functional rescue experiment; single lab, single method for direct interaction","pmids":["31288830"],"is_preprint":false},{"year":2020,"finding":"Ubl4A promotes mitochondrial fusion under nutrient deprivation via its interaction with the Arp2/3 complex. Ubl4A deficiency reduces the primed Arp2/3 complex pool around mitochondria, impairs fusion, causes mitochondrial fragmentation, ROS accumulation, and caspase 9-dependent apoptosis. An Arp2/3-binding-deficient Ubl4A mutant fails to rescue this phenotype.","method":"Ubl4A KO cells and rescue with wild-type vs. Arp2/3-binding mutant, mitochondrial morphology imaging, ROS measurement, caspase 9 activity assay","journal":"PLoS ONE","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with specific phenotype, domain-mutant rescue experiment, multiple readouts; single lab","pmids":["33211772"],"is_preprint":false},{"year":2023,"finding":"Disease-associated polyglutamine inclusions disrupt formation of the BAG6-UBL4A complex. UBL4A also dissociates from BAG6 in response to proteasomal inhibition and mitochondrial depolarization (proteotoxic stresses), implying that disruption of the BAG6-UBL4A complex contributes to impaired TA protein biogenesis under stress.","method":"Co-immunoprecipitation under proteotoxic stress conditions (polyglutamine, proteasome inhibitor, mitochondrial depolarizing agent)","journal":"Biochemical Journal","confidence":"Medium","confidence_rationale":"Tier 2/3 / Weak — co-IP under multiple stress conditions, single lab, single study","pmids":["37747814"],"is_preprint":false},{"year":2007,"finding":"Yeast Mdy2 (UBL4A ortholog) interacts with the N-terminal region of Sgt2, and Mdy2 also physically interacts with the chaperone Ydj1, potentially mediating association between Ydj1 and Sgt2. MDY2 interacts genetically with YDJ1.","method":"Co-immunoprecipitation, genetic interaction (synthetic lethality/mating efficiency assay)","journal":"Cell Stress & Chaperones","confidence":"Medium","confidence_rationale":"Tier 2/3 / Moderate — co-IP plus genetic epistasis, two orthogonal methods; single lab","pmids":["17441508"],"is_preprint":false},{"year":2006,"finding":"Yeast Mdy2 (UBL4A ortholog) contains a UBL domain but shows no evidence of C-terminal processing typical of ubiquitin. In mdy2Δ cells, microtubule bundles and the MT end-binding protein Kar9 fail to localize properly to the shmoo tip, causing defects in nuclear migration and karyogamy during mating.","method":"Deletion mutant phenotypic analysis, GFP localization, His-tag processing assay, immunofluorescence of microtubules and Kar9","journal":"Journal of Cell Science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with specific cellular phenotype (nuclear migration, Kar9 mislocalization), direct localization experiments; single lab","pmids":["16390866"],"is_preprint":false},{"year":2010,"finding":"Yeast Mdy2 (UBL4A ortholog) associates with α-tubulin and the dynactin subunit p150(Glued)/Nip100. Under heat stress, nuclear Mdy2 relocalizes to cytoplasmic stress granules co-marked by Pab1 (poly(A)-binding protein).","method":"Co-precipitation, GFP live imaging, colocalization with stress granule markers","journal":"Cytoskeleton","confidence":"Medium","confidence_rationale":"Tier 2/3 / Moderate — co-precipitation and live-cell imaging, two orthogonal methods; single lab","pmids":["20722039"],"is_preprint":false},{"year":2012,"finding":"Nuclear import of yeast Mdy2 (UBL4A ortholog) is mediated by an N-terminal nuclear localization signal (NLS) and is required for heat stress response. Mdy2 physically interacts with Pab1 and this interaction (and accumulation in stress granules) depends on nuclear history (NLS intact), not nuclear retention (NES deletion has no effect).","method":"NLS/NES deletion mutants, GFP localization, co-precipitation with Pab1, heat stress viability assays","journal":"PLoS ONE","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain-deletion mutants with localization and functional readouts plus co-precipitation; single lab","pmids":["23285234"],"is_preprint":false},{"year":2013,"finding":"Crystal structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain (yeast) reveals one Sgt2 dimer binding one Get5 monomer via hydrophobic residues from both proteins; these hydrophobic interface residues are important for cell survival under heat stress.","method":"Crystal structure, mutagenesis, heat stress cell survival assay","journal":"Acta Crystallographica Section D","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with mutagenesis and functional in vivo validation; single lab","pmids":["24100326"],"is_preprint":false},{"year":2024,"finding":"GdX/UBL4A directly interacts with STAT3 (confirmed by dual-luciferase reporter and immunofluorescence) and overexpression of GdX reduces phosphorylation of STAT3, inhibiting downstream STAT3 target genes BCL-XL, Cyclin D1, and c-Myc in breast cancer cells.","method":"Dual-luciferase reporter assay, immunofluorescence co-localization, western blot phosphorylation assay, KO mouse tumor model","journal":"Cancer Biology & Therapy","confidence":"Low","confidence_rationale":"Tier 3 / Weak — reporter assay and IF for interaction, no direct binding assay (e.g., co-IP or pull-down reported in abstract); single lab","pmids":["39487760"],"is_preprint":false},{"year":2011,"finding":"In yeast, sgt2Δ get5Δ double mutants show more severe TA protein sorting defects than either single knockout, indicating cooperative functions. Overproduction of Sgt2 is toxic in get3Δ but not get5Δ cells, indicating a Get5-independent role for Sgt2 in TA protein delivery to Get3.","method":"Genetic epistasis (double-mutant analysis), TA protein sorting assays, overexpression toxicity assay","journal":"Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with defined phenotypic readout, multiple mutant combinations tested; single lab","pmids":["21619481"],"is_preprint":false}],"current_model":"UBL4A (GdX/Get5/Mdy2) is a ubiquitin-like domain protein that functions as a core subunit of the BAG6–UBL4A–TRC35/GET4 holdase complex, where its UBL domain directly and electrostatically engages the N-terminal dimerization domain of SGTA/Sgt2 to facilitate handoff of tail-anchored (TA) proteins toward the ER membrane; within the GET/TRC pathway, the Get4–Get5 complex positions Get5/UBL4A upstream of Get3/TRC40 and uses Get4 to regulate Get3 ATPase activity for optimal TA substrate capture, as established by multiple crystal structures and biochemical reconstitutions. Beyond TA protein biogenesis, UBL4A directly binds the Arp2/3 complex via its C-terminus (critical residue D122) to promote actin branching, enabling insulin-induced Akt plasma membrane translocation, cell migration, and mitochondrial fusion under nutrient stress. Additional mechanistic roles include: disrupting the TC45/PP2A/p65 complex to sustain NF-κB p65 phosphorylation in innate immune cells; promoting K63-linked ubiquitination of TRAF6 to enhance antiviral IFN signaling; directly interacting with LAMP1 to impair lysosomal function and autophagy; translocating to the nucleus with BAG6 upon DNA damage to support BRCA1 recruitment and damage-induced cell death; and, in yeast, mediating nuclear import-dependent stress granule formation and microtubule-dependent nuclear migration via association with α-tubulin and dynactin."},"narrative":{"mechanistic_narrative":"UBL4A (GdX/Get5/Mdy2) is a ubiquitin-like domain adaptor that operates at the core of the cytosolic machinery delivering tail-anchored (TA) membrane proteins to the ER, while also serving as a versatile scaffold in actin dynamics, immune signaling, and nuclear stress responses [PMID:23142665, PMID:26195787]. Within the BAG6-UBL4A-TRC35/GET4 holdase pathway, the unconventional UBL domain of UBL4A engages the N-terminal dimerization domain of SGTA/Sgt2 through a high-affinity electrostatic and hydrophobic interface (one UBL per SGTA dimer), recruiting SGTA to the BAG6 complex to enhance substrate loading and prevent nondegradable aggregates during ERAD [PMID:23246001, PMID:23142665, PMID:23297211, PMID:24100326]. In the upstream targeting step, the Get4-Get5/UBL4A subcomplex positions Get3/TRC40 and uses Get4 to prime Get3 ATPase activity for optimal TA-substrate capture [PMID:20554915, PMID:20106980, PMID:24727835]. UBL4A binds the BAG6 C-terminus through a distinct BAGS-domain interface that controls UBL4A stability, and proteotoxic stresses such as polyglutamine inclusions, proteasome inhibition, and mitochondrial depolarization dissociate the BAG6-UBL4A complex [PMID:25713138, PMID:37747814]. Beyond protein biogenesis, UBL4A directly binds the Arp2/3 complex via its C-terminus—a contact requiring residue D122—to drive actin branching, supporting insulin-induced Akt plasma-membrane translocation and glycogen synthesis, cell migration, and stress-induced mitochondrial fusion [PMID:26195787, PMID:30146258, PMID:33211772]. UBL4A additionally tunes innate immunity by trapping TC45/PTPN2 to sustain NF-κB p65 phosphorylation and by promoting K63-linked ubiquitination of TRAF6 to enhance type I IFN signaling [PMID:30867837, PMID:31451677], and translocates to the nucleus with BAG6 upon DNA damage to support BRCA1 recruitment and damage-induced cell death [PMID:23723067]. In yeast, the ortholog mediates NLS-dependent nuclear import, heat-stress stress-granule formation via Pab1, and microtubule-dependent nuclear migration through association with α-tubulin and dynactin [PMID:16390866, PMID:20722039, PMID:23285234].","teleology":[{"year":2006,"claim":"Established that the UBL4A ortholog is a UBL-domain protein lacking canonical ubiquitin processing and is needed for cytoskeletal organization, answering whether this UBL behaves like ubiquitin or has a distinct cellular role.","evidence":"Yeast mdy2Δ deletion phenotyping, His-tag processing assay, and microtubule/Kar9 immunofluorescence","pmids":["16390866"],"confidence":"Medium","gaps":["Molecular basis linking Mdy2 to microtubule/Kar9 localization not defined","Relevance to mammalian UBL4A function untested"]},{"year":2007,"claim":"Identified the Sgt2 N-terminus and the chaperone Ydj1 as physical partners of the ortholog, placing it within a chaperone-adaptor network rather than acting alone.","evidence":"Co-immunoprecipitation and genetic interaction assays in yeast","pmids":["17441508"],"confidence":"Medium","gaps":["Direct vs. bridged nature of the Ydj1 association unresolved","Structural interface undefined"]},{"year":2010,"claim":"Positioned Get4/Get5 upstream of Get3 in the TA-targeting pathway by showing nucleotide-dependent Get3 binding to a conserved Get4 surface, defining the pathway's directional architecture.","evidence":"Crystal structure of the Get4/Get5 N-terminal fragment with ITC and co-IP","pmids":["20554915","20106980"],"confidence":"High","gaps":["How substrate is handed from Get5/Sgt2 to Get3 not yet resolved at this stage"]},{"year":2010,"claim":"Linked the ortholog to cytoskeletal and stress-granule machinery, showing it associates with α-tubulin and dynactin and relocalizes to stress granules under heat, expanding its role beyond TA targeting.","evidence":"Co-precipitation and GFP live imaging with stress-granule markers in yeast","pmids":["20722039"],"confidence":"Medium","gaps":["Functional consequence of tubulin/dynactin binding unclear","Whether mammalian UBL4A shares these contacts untested"]},{"year":2011,"claim":"Distinguished cooperative from independent roles of Sgt2 and Get5, showing they act together in TA sorting yet Sgt2 retains a Get5-independent delivery function to Get3.","evidence":"Genetic epistasis of sgt2Δ get5Δ double mutants and overexpression toxicity assays","pmids":["21619481"],"confidence":"Medium","gaps":["Biochemical basis of the Get5-independent route not defined"]},{"year":2012,"claim":"Defined the molecular handshake of the pathway: the noncanonical SGTA UBD engages the unconventional UBL4A UBL domain via electrostatics, recruiting SGTA to BAG6 and preventing aggregate formation during ERAD.","evidence":"NMR, crystal structures (yeast and human), ITC, chemical shift perturbation, and co-IP across two studies","pmids":["23246001","23142665"],"confidence":"High","gaps":["Substrate transfer dynamics across the interface not directly visualized"]},{"year":2012,"claim":"Established NLS-dependent nuclear import as a prerequisite for the ortholog's heat-stress response and Pab1 interaction, revealing a nuclear-history requirement for its stress function.","evidence":"NLS/NES deletion mutants, GFP localization, co-precipitation with Pab1, and heat-stress viability in yeast","pmids":["23285234"],"confidence":"Medium","gaps":["Why nuclear transit is required for cytoplasmic stress-granule function is unexplained"]},{"year":2013,"claim":"Resolved the binding stoichiometry and atomic interface (1 Sgt2 dimer : 1 Get5 UBL) and validated the contact residues, providing structural ground truth for the SGTA-UBL4A complex.","evidence":"NMR solution structure, crystal structure, ITC, and site-directed mutagenesis","pmids":["23297211","24100326"],"confidence":"High","gaps":["Conformational changes during substrate loading not captured"]},{"year":2013,"claim":"Extended UBL4A into the DNA-damage response, showing nuclear translocation with BAG6/GET4 and a requirement for BRCA1 recruitment and damage-induced cell death.","evidence":"siRNA knockdown, viability assays, immunofluorescence, and BRCA1 recruitment assays","pmids":["23723067"],"confidence":"Medium","gaps":["Direct mechanistic link between the complex and BRCA1 recruitment undefined","Single-lab finding"]},{"year":2014,"claim":"Showed how the pathway is kinetically regulated: Get4 primes Get3 in an ATP-bound ternary complex to optimize TA-substrate capture, defining the catalytic logic of targeting.","evidence":"Crystal structure of the Get3-Get4-Get5 ternary complex with ATPase and structure-guided assays","pmids":["24727835"],"confidence":"High","gaps":["Full hand-off to the ER membrane downstream of Get3 not captured in this complex"]},{"year":2014,"claim":"Demonstrated that UBL4A and BAG6 UBL domains compete for the same SGTA site, establishing a regulatory switch at the SGTA dimerization domain.","evidence":"NMR structure, ITC, microscale thermophoresis, and HADDOCK docking","pmids":["25415308"],"confidence":"High","gaps":["Physiological trigger that selects UBL4A vs. BAG6 occupancy unknown"]},{"year":2015,"claim":"Defined the BAG6-UBL4A heterodimerization through a novel C-terminal BAGS interface and showed BAG6 binding stabilizes UBL4A, explaining co-dependence of complex members.","evidence":"Crystal structure with biochemical and cell-based stability assays","pmids":["25713138"],"confidence":"High","gaps":["How stability control feeds back on TA-targeting flux not addressed"]},{"year":2015,"claim":"Opened a TA-independent role by showing UBL4A directly binds Arp2/3 to accelerate actin branching, enabling insulin-induced Akt membrane translocation and glycogen synthesis.","evidence":"In vitro actin branching, interaction assays, Ubl4A KO mouse, and live-cell Akt imaging","pmids":["26195787"],"confidence":"High","gaps":["Whether the UBL and Arp2/3-binding functions are spatially partitioned in cells unclear"]},{"year":2016,"claim":"Generalized the actin role to motility, showing UBL4A loss impairs membrane protrusion, fibroblast and macrophage migration, and wound healing.","evidence":"Ubl4A KO mouse, wound-healing, ex vivo migration, and motility assays","pmids":["27998771"],"confidence":"Medium","gaps":["Direct dependence on Arp2/3 binding not tested with domain mutants here"]},{"year":2018,"claim":"Mapped the Arp2/3 contact to the UBL4A C-terminus and identified D122 as the critical residue whose mutation abolishes binding, destabilizes the protein, and removes pro-death activity in colon cancer.","evidence":"In vitro pull-down, D122A mutagenesis, and cell death assays","pmids":["30146258"],"confidence":"Medium","gaps":["Structural basis of D122-mediated Arp2/3 contact not solved","Single-study finding"]},{"year":2019,"claim":"Assigned UBL4A an immune-signaling role by trapping TC45/PTPN2 to disrupt the phosphatase complex that dephosphorylates p65, sustaining NF-κB activation.","evidence":"Reciprocal co-IP, luciferase reporters, and tissue-specific KO mice in LPS and DSS colitis models","pmids":["30867837"],"confidence":"Medium","gaps":["Whether this competes with TA-targeting functions of UBL4A unknown"]},{"year":2019,"claim":"Extended immune function to antiviral signaling, showing UBL4A binds TRAF6 and promotes its K63-linked ubiquitination to amplify type I IFN responses.","evidence":"Co-IP, K63-specific ubiquitination assays, knockdown/overexpression, and phosphorylation blots","pmids":["31451677"],"confidence":"Medium","gaps":["Whether UBL4A acts as or recruits the E3 ligase for TRAF6 not determined"]},{"year":2019,"claim":"Linked UBL4A to lysosomal control by showing direct LAMP1 interaction that impairs lysosomal function and autophagic degradation in pancreatic cancer.","evidence":"Co-IP, autophagy marker blots, and in vitro/orthotopic functional rescue","pmids":["31288830"],"confidence":"Medium","gaps":["Single Co-IP method for direct interaction without reciprocal structural validation","Mechanism of LAMP1-mediated lysosomal impairment unclear"]},{"year":2020,"claim":"Tied the Arp2/3 axis to mitochondrial homeostasis, showing UBL4A promotes nutrient-stress mitochondrial fusion and that an Arp2/3-binding-deficient mutant fails to rescue fragmentation and apoptosis.","evidence":"Ubl4A KO cells with WT vs. Arp2/3-binding mutant rescue, mitochondrial imaging, ROS, and caspase-9 assays","pmids":["33211772"],"confidence":"Medium","gaps":["How perimitochondrial primed Arp2/3 drives fusion mechanically not defined"]},{"year":2023,"claim":"Showed that the BAG6-UBL4A complex is disrupted by proteotoxic stress, connecting complex integrity to impaired TA biogenesis under disease-relevant conditions.","evidence":"Co-IP under polyglutamine, proteasome inhibition, and mitochondrial depolarization","pmids":["37747814"],"confidence":"Medium","gaps":["Functional consequence on TA-protein flux measured indirectly","Single-study finding"]},{"year":2024,"claim":"Proposed a UBL4A-STAT3 axis in which UBL4A reduces STAT3 phosphorylation and downstream oncogenic target expression in breast cancer.","evidence":"Dual-luciferase reporter, immunofluorescence colocalization, phosphorylation blots, and KO mouse tumor model","pmids":["39487760"],"confidence":"Low","gaps":["No direct binding assay (co-IP/pull-down) reported for the UBL4A-STAT3 interaction","Single-lab study"]},{"year":null,"claim":"How UBL4A partitions among its multiple roles—TA-protein holdase, Arp2/3-driven actin scaffold, immune signaling regulator, and nuclear damage-response factor—and what governs the switch between them remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model coordinating cytosolic, immune, and nuclear functions","Structural basis of the C-terminal Arp2/3 contact unsolved","Triggers selecting BAG6 vs. SGTA vs. non-canonical partners unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,5]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[8,10,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,11]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,2,8]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[7,19]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[1,2,4]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,5,15]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[11,12]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[13]}],"complexes":["BAG6-UBL4A-TRC35/GET4 holdase complex","Get3-Get4-Get5 targeting complex"],"partners":["SGTA","BAG6","GET4","GET3","ARPC (ARP2/3 COMPLEX)","TRAF6","PTPN2","LAMP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P11441","full_name":"Ubiquitin-like protein 4A","aliases":["Ubiquitin-like protein GDX"],"length_aa":157,"mass_kda":17.8,"function":"As part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and participates in their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation (PubMed:20676083, PubMed:21636303, PubMed:21743475, PubMed:28104892). The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane. Recruited to ribosomes, it interacts with the transmembrane region of newly synthesized tail-anchored proteins and together with SGTA and ASNA1 mediates their delivery to the endoplasmic reticulum (PubMed:20676083, PubMed:25535373, PubMed:28104892). Client proteins that cannot be properly delivered to the endoplasmic reticulum are ubiquitinated and sorted to the proteasome (PubMed:28104892). Similarly, the BAG6/BAT3 complex also functions as a sorting platform for proteins of the secretory pathway that are mislocalized to the cytosol either delivering them to the proteasome for degradation or to the endoplasmic reticulum (PubMed:21743475). The BAG6/BAT3 complex also plays a role in the endoplasmic reticulum-associated degradation (ERAD), a quality control mechanism that eliminates unwanted proteins of the endoplasmic reticulum through their retrotranslocation to the cytosol and their targeting to the proteasome. It maintains these retrotranslocated proteins in an unfolded yet soluble state condition in the cytosol to ensure their proper delivery to the proteasome (PubMed:21636303)","subcellular_location":"Cytoplasm, cytosol; Nucleus","url":"https://www.uniprot.org/uniprotkb/P11441/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBL4A","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"GET4","stoichiometry":10.0},{"gene":"RAB11A","stoichiometry":10.0},{"gene":"BAG6","stoichiometry":4.0},{"gene":"RAB7A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBL4A","total_profiled":1310},"omim":[{"mim_id":"620200","title":"CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIy; CDG2Y","url":"https://www.omim.org/entry/620200"},{"mim_id":"612056","title":"GUIDED ENTRY OF TAIL-ANCHORED PROTEINS FACTOR 4; GET4","url":"https://www.omim.org/entry/612056"},{"mim_id":"611127","title":"UBIQUITIN-LIKE 4B; UBL4B","url":"https://www.omim.org/entry/611127"},{"mim_id":"601913","title":"GUIDED ENTRY OF TAIL-ANCHORED PROTEINS FACTOR 3, ATPase; GET3","url":"https://www.omim.org/entry/601913"},{"mim_id":"601118","title":"CALCIUM-MODULATING LIGAND; CAMLG","url":"https://www.omim.org/entry/601118"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBL4A"},"hgnc":{"alias_symbol":["GDX","DXS254E","GET5","MDY2","TMA24"],"prev_symbol":["UBL4"]},"alphafold":{"accession":"P11441","domains":[{"cath_id":"3.10.20.90","chopping":"1-73","consensus_level":"high","plddt":88.8786,"start":1,"end":73},{"cath_id":"-","chopping":"93-152","consensus_level":"high","plddt":81.389,"start":93,"end":152}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P11441","model_url":"https://alphafold.ebi.ac.uk/files/AF-P11441-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P11441-F1-predicted_aligned_error_v6.png","plddt_mean":79.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBL4A","jax_strain_url":"https://www.jax.org/strain/search?query=UBL4A"},"sequence":{"accession":"P11441","fasta_url":"https://rest.uniprot.org/uniprotkb/P11441.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P11441/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P11441"}},"corpus_meta":[{"pmid":"23246001","id":"PMC_23246001","title":"SGTA 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Section D, Biological crystallography","url":"https://pubmed.ncbi.nlm.nih.gov/24100326","citation_count":9,"is_preprint":false},{"pmid":"37994026","id":"PMC_37994026","title":"Circ_0006944 aggravates LPS-induced HK2 cell injury via modulating miR-205-5p/UBL4A pathway.","date":"2023","source":"Autoimmunity","url":"https://pubmed.ncbi.nlm.nih.gov/37994026","citation_count":8,"is_preprint":false},{"pmid":"31451677","id":"PMC_31451677","title":"UBL4A Augments Innate Immunity by Promoting the K63-Linked Ubiquitination of TRAF6.","date":"2019","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/31451677","citation_count":8,"is_preprint":false},{"pmid":"31002527","id":"PMC_31002527","title":"GdX/UBL4A-knockout mice resist collagen-induced arthritis by balancing the population of Th1/Th17 and regulatory T cells.","date":"2019","source":"FASEB journal : official publication of the Federation of American Societies for Experimental 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This interaction recruits SGTA to the BAG6 complex, enhances substrate loading to BAG6, and prevents formation of nondegradable protein aggregates during ERAD.\",\n      \"method\": \"NMR spectroscopy, biochemical binding assays, co-immunoprecipitation\",\n      \"journal\": \"Cell Reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 / Strong — NMR structure determination combined with biochemical assays; replicated across multiple studies (PMIDs 23142665, 23297211, 25415308)\",\n      \"pmids\": [\"23246001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Get4 (TRC35) and Get5 (UBL4A/Mdy2) form a tight complex in yeast, and Get3 specifically binds to a conserved surface on Get4 in a nucleotide-dependent manner, placing Get4/5 upstream of Get3 in the tail-anchored protein targeting pathway.\",\n      \"method\": \"Crystal structure of Get4/Get5 N-terminal fragment, co-immunoprecipitation, isothermal titration calorimetry\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus biochemical validation; independently replicated by Chang et al. (PMID 20106980)\",\n      \"pmids\": [\"20554915\", \"20106980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The N-terminal dimerization domain of Sgt2/SGTA directly binds the UBL domain of Get5/UBL4A via electrostatics, forming a high-affinity complex with rapid kinetics, structurally characterized for both yeast and human protein pairs.\",\n      \"method\": \"Crystal structures (yeast and human UBD/UBL complex), biophysical studies (ITC, NMR chemical shift perturbation)\",\n      \"journal\": \"Cell Reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures for both yeast and human proteins, multiple orthogonal biophysical methods, independently replicated (PMIDs 23246001, 23297211, 24100326, 25415308)\",\n      \"pmids\": [\"23142665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Solution structure of Sgt2_NT (unique helical fold) and crystal structure of Get5_UBL determined; NMR chemical shift perturbation and ITC establish a 1:2 stoichiometry (one Get5 UBL to one Sgt2 dimer); site-directed mutagenesis validated the binding interface.\",\n      \"method\": \"NMR solution structure, crystal structure, isothermal titration calorimetry, site-directed mutagenesis, relaxation experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal structural and biophysical methods with mutagenesis validation in a single rigorous study\",\n      \"pmids\": [\"23297211\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of yeast Get3-Get4-Get5 ternary complex in an ATP-bound state reveals that Get4 primes Get3 by promoting an optimal configuration for TA substrate capture; Get4-mediated regulation of Get3 ATP hydrolysis is essential for efficient TA-protein targeting.\",\n      \"method\": \"Crystal structure, structure-guided biochemical assays, ATPase activity measurements\",\n      \"journal\": \"Nature Structural & Molecular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of ternary complex combined with structure-guided mutagenesis and functional assays in a single high-rigor study\",\n      \"pmids\": [\"24727835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the C-terminal heterodimerization domains of BAG6 and Ubl4A reveals a novel binding interface; the BAG6 C-terminus (designated BAGS domain) is structurally distinct from canonical BAG domains. Tight association of BAG6 and Ubl4A modulates Ubl4A protein stability in cells.\",\n      \"method\": \"Crystal structure, biochemical binding assays, cell-based stability assays\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with biochemical and cell-based validation in a single study\",\n      \"pmids\": [\"25713138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NMR solution structure of the SGTA dimerization domain determined; UBL domains from UBL4A and BAG6 compete for binding to SGTA at the same site, characterized by NMR chemical shift perturbation, ITC, and microscale thermophoresis; HADDOCK docking models of SGTA-UBL complexes generated.\",\n      \"method\": \"NMR structure determination, ITC, microscale thermophoresis, NMR chemical shift perturbation\",\n      \"journal\": \"PLoS ONE\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with three independent biophysical methods for interaction characterization\",\n      \"pmids\": [\"25415308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Nuclear BAG6-UBL4A-GET4 complex mediates DNA damage signaling and cell death. Upon DNA damage, UBL4A and GET4 translocate to the nucleus. Depletion of BAG6 causes loss of both UBL4A and GET4 proteins. Co-depletion of UBL4A and GET4 (but not single depletion) confers resistance to DNA damage-induced cell death. All three components regulate BRCA1 recruitment to DNA damage sites.\",\n      \"method\": \"siRNA knockdown, cell viability assays, immunofluorescence for nuclear translocation, BRCA1 recruitment assays\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined cellular phenotype, multiple functional readouts, single lab\",\n      \"pmids\": [\"23723067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Ubl4A directly interacts with the Arp2/3 complex to accelerate actin branching and networking, enabling insulin-induced Akt translocation to the plasma membrane. Ubl4A knockout mice have defective Akt-dependent glycogen synthesis. Akt binds actin filaments and colocalizes with Arp2/3 in membrane ruffles.\",\n      \"method\": \"Protein-protein interaction assays, actin branching in vitro assays, Ubl4A knockout mouse model, live-cell imaging of Akt translocation, glycogen synthesis assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 / Strong — in vitro actin branching assay, direct interaction demonstrated, KO mouse with defined metabolic phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"26195787\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Ubl4A, F-actin, and Arp2/3 co-localize at cell leading edges during wound closure. Knockout of Ubl4A reduces actin-mediated membrane protrusion, delays wound healing in primary mouse embryonic fibroblasts, impairs fibroblast migration from corneal tissue ex vivo, and decreases macrophage motility without affecting phagocytosis.\",\n      \"method\": \"Ubl4A KO mouse model, wound-healing assay, immunofluorescence co-localization, ex vivo migration assay, macrophage motility and phagocytosis assays\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse with specific cellular phenotype, multiple cell types and assays, single lab\",\n      \"pmids\": [\"27998771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The C-terminal region of Ubl4A directly interacts with the Arp2/3 complex in pull-down assays. A point mutation D122A in the C-terminus abolishes Arp2/3 binding and destabilizes Ubl4A. Wild-type Ubl4A induces cell death in colon cancer cells via its C-terminal Arp2/3-binding activity, while D122A mutant loses this pro-death activity.\",\n      \"method\": \"In vitro protein pull-down, site-directed mutagenesis (D122A), cell death assays\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1/2 / Weak — in vitro pull-down with mutagenesis, cell-based functional validation, single lab single study\",\n      \"pmids\": [\"30146258\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"GdX/UBL4A positively regulates NF-κB signaling in dendritic cells and macrophages by trapping TC45 (PTPN2), thereby disrupting the TC45/PP2A/p65 complex that mediates p65 dephosphorylation and preventing p65 dephosphorylation.\",\n      \"method\": \"Immunoprecipitation, luciferase reporter assay, LPS challenge of GdX-deficient mice, cytokine ELISA, DSS colitis model with tissue-specific KO mice\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP, reporter assay, and in vivo KO models with defined immune phenotype; single lab\",\n      \"pmids\": [\"30867837\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"UBL4A interacts with TRAF6 via co-immunoprecipitation, and this interaction is enhanced upon viral infection. UBL4A promotes K63-linked ubiquitination of TRAF6, enhancing TBK1, IRF3, and IKKα/β phosphorylation and type I IFN transcription.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K63-specific), siRNA knockdown and overexpression, phosphorylation western blots\",\n      \"journal\": \"Journal of Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus K63-specific ubiquitination assay and functional phosphorylation readouts; single lab\",\n      \"pmids\": [\"31451677\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"UBL4A directly interacts with LAMP1 by co-immunoprecipitation and causes lysosomal dysfunction leading to impaired autophagic degradation and autophagosome accumulation in pancreatic cancer cells. LAMP1 overexpression reverses the antitumor effects of UBL4A.\",\n      \"method\": \"Co-immunoprecipitation, western blot autophagy markers, in vitro and in vivo (orthotopic) functional assays\",\n      \"journal\": \"Journal of Experimental & Clinical Cancer Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Moderate — co-IP with functional rescue experiment; single lab, single method for direct interaction\",\n      \"pmids\": [\"31288830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Ubl4A promotes mitochondrial fusion under nutrient deprivation via its interaction with the Arp2/3 complex. Ubl4A deficiency reduces the primed Arp2/3 complex pool around mitochondria, impairs fusion, causes mitochondrial fragmentation, ROS accumulation, and caspase 9-dependent apoptosis. An Arp2/3-binding-deficient Ubl4A mutant fails to rescue this phenotype.\",\n      \"method\": \"Ubl4A KO cells and rescue with wild-type vs. Arp2/3-binding mutant, mitochondrial morphology imaging, ROS measurement, caspase 9 activity assay\",\n      \"journal\": \"PLoS ONE\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with specific phenotype, domain-mutant rescue experiment, multiple readouts; single lab\",\n      \"pmids\": [\"33211772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Disease-associated polyglutamine inclusions disrupt formation of the BAG6-UBL4A complex. UBL4A also dissociates from BAG6 in response to proteasomal inhibition and mitochondrial depolarization (proteotoxic stresses), implying that disruption of the BAG6-UBL4A complex contributes to impaired TA protein biogenesis under stress.\",\n      \"method\": \"Co-immunoprecipitation under proteotoxic stress conditions (polyglutamine, proteasome inhibitor, mitochondrial depolarizing agent)\",\n      \"journal\": \"Biochemical Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Weak — co-IP under multiple stress conditions, single lab, single study\",\n      \"pmids\": [\"37747814\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Yeast Mdy2 (UBL4A ortholog) interacts with the N-terminal region of Sgt2, and Mdy2 also physically interacts with the chaperone Ydj1, potentially mediating association between Ydj1 and Sgt2. MDY2 interacts genetically with YDJ1.\",\n      \"method\": \"Co-immunoprecipitation, genetic interaction (synthetic lethality/mating efficiency assay)\",\n      \"journal\": \"Cell Stress & Chaperones\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Moderate — co-IP plus genetic epistasis, two orthogonal methods; single lab\",\n      \"pmids\": [\"17441508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Yeast Mdy2 (UBL4A ortholog) contains a UBL domain but shows no evidence of C-terminal processing typical of ubiquitin. In mdy2Δ cells, microtubule bundles and the MT end-binding protein Kar9 fail to localize properly to the shmoo tip, causing defects in nuclear migration and karyogamy during mating.\",\n      \"method\": \"Deletion mutant phenotypic analysis, GFP localization, His-tag processing assay, immunofluorescence of microtubules and Kar9\",\n      \"journal\": \"Journal of Cell Science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with specific cellular phenotype (nuclear migration, Kar9 mislocalization), direct localization experiments; single lab\",\n      \"pmids\": [\"16390866\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Yeast Mdy2 (UBL4A ortholog) associates with α-tubulin and the dynactin subunit p150(Glued)/Nip100. Under heat stress, nuclear Mdy2 relocalizes to cytoplasmic stress granules co-marked by Pab1 (poly(A)-binding protein).\",\n      \"method\": \"Co-precipitation, GFP live imaging, colocalization with stress granule markers\",\n      \"journal\": \"Cytoskeleton\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Moderate — co-precipitation and live-cell imaging, two orthogonal methods; single lab\",\n      \"pmids\": [\"20722039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Nuclear import of yeast Mdy2 (UBL4A ortholog) is mediated by an N-terminal nuclear localization signal (NLS) and is required for heat stress response. Mdy2 physically interacts with Pab1 and this interaction (and accumulation in stress granules) depends on nuclear history (NLS intact), not nuclear retention (NES deletion has no effect).\",\n      \"method\": \"NLS/NES deletion mutants, GFP localization, co-precipitation with Pab1, heat stress viability assays\",\n      \"journal\": \"PLoS ONE\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain-deletion mutants with localization and functional readouts plus co-precipitation; single lab\",\n      \"pmids\": [\"23285234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain (yeast) reveals one Sgt2 dimer binding one Get5 monomer via hydrophobic residues from both proteins; these hydrophobic interface residues are important for cell survival under heat stress.\",\n      \"method\": \"Crystal structure, mutagenesis, heat stress cell survival assay\",\n      \"journal\": \"Acta Crystallographica Section D\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with mutagenesis and functional in vivo validation; single lab\",\n      \"pmids\": [\"24100326\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"GdX/UBL4A directly interacts with STAT3 (confirmed by dual-luciferase reporter and immunofluorescence) and overexpression of GdX reduces phosphorylation of STAT3, inhibiting downstream STAT3 target genes BCL-XL, Cyclin D1, and c-Myc in breast cancer cells.\",\n      \"method\": \"Dual-luciferase reporter assay, immunofluorescence co-localization, western blot phosphorylation assay, KO mouse tumor model\",\n      \"journal\": \"Cancer Biology & Therapy\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — reporter assay and IF for interaction, no direct binding assay (e.g., co-IP or pull-down reported in abstract); single lab\",\n      \"pmids\": [\"39487760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In yeast, sgt2Δ get5Δ double mutants show more severe TA protein sorting defects than either single knockout, indicating cooperative functions. Overproduction of Sgt2 is toxic in get3Δ but not get5Δ cells, indicating a Get5-independent role for Sgt2 in TA protein delivery to Get3.\",\n      \"method\": \"Genetic epistasis (double-mutant analysis), TA protein sorting assays, overexpression toxicity assay\",\n      \"journal\": \"Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with defined phenotypic readout, multiple mutant combinations tested; single lab\",\n      \"pmids\": [\"21619481\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBL4A (GdX/Get5/Mdy2) is a ubiquitin-like domain protein that functions as a core subunit of the BAG6–UBL4A–TRC35/GET4 holdase complex, where its UBL domain directly and electrostatically engages the N-terminal dimerization domain of SGTA/Sgt2 to facilitate handoff of tail-anchored (TA) proteins toward the ER membrane; within the GET/TRC pathway, the Get4–Get5 complex positions Get5/UBL4A upstream of Get3/TRC40 and uses Get4 to regulate Get3 ATPase activity for optimal TA substrate capture, as established by multiple crystal structures and biochemical reconstitutions. Beyond TA protein biogenesis, UBL4A directly binds the Arp2/3 complex via its C-terminus (critical residue D122) to promote actin branching, enabling insulin-induced Akt plasma membrane translocation, cell migration, and mitochondrial fusion under nutrient stress. Additional mechanistic roles include: disrupting the TC45/PP2A/p65 complex to sustain NF-κB p65 phosphorylation in innate immune cells; promoting K63-linked ubiquitination of TRAF6 to enhance antiviral IFN signaling; directly interacting with LAMP1 to impair lysosomal function and autophagy; translocating to the nucleus with BAG6 upon DNA damage to support BRCA1 recruitment and damage-induced cell death; and, in yeast, mediating nuclear import-dependent stress granule formation and microtubule-dependent nuclear migration via association with α-tubulin and dynactin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBL4A (GdX/Get5/Mdy2) is a ubiquitin-like domain adaptor that operates at the core of the cytosolic machinery delivering tail-anchored (TA) membrane proteins to the ER, while also serving as a versatile scaffold in actin dynamics, immune signaling, and nuclear stress responses [#2, #8]. Within the BAG6-UBL4A-TRC35/GET4 holdase pathway, the unconventional UBL domain of UBL4A engages the N-terminal dimerization domain of SGTA/Sgt2 through a high-affinity electrostatic and hydrophobic interface (one UBL per SGTA dimer), recruiting SGTA to the BAG6 complex to enhance substrate loading and prevent nondegradable aggregates during ERAD [#0, #2, #3, #20]. In the upstream targeting step, the Get4-Get5/UBL4A subcomplex positions Get3/TRC40 and uses Get4 to prime Get3 ATPase activity for optimal TA-substrate capture [#1, #4]. UBL4A binds the BAG6 C-terminus through a distinct BAGS-domain interface that controls UBL4A stability, and proteotoxic stresses such as polyglutamine inclusions, proteasome inhibition, and mitochondrial depolarization dissociate the BAG6-UBL4A complex [#5, #15]. Beyond protein biogenesis, UBL4A directly binds the Arp2/3 complex via its C-terminus—a contact requiring residue D122—to drive actin branching, supporting insulin-induced Akt plasma-membrane translocation and glycogen synthesis, cell migration, and stress-induced mitochondrial fusion [#8, #10, #14]. UBL4A additionally tunes innate immunity by trapping TC45/PTPN2 to sustain NF-\\u03baB p65 phosphorylation and by promoting K63-linked ubiquitination of TRAF6 to enhance type I IFN signaling [#11, #12], and translocates to the nucleus with BAG6 upon DNA damage to support BRCA1 recruitment and damage-induced cell death [#7]. In yeast, the ortholog mediates NLS-dependent nuclear import, heat-stress stress-granule formation via Pab1, and microtubule-dependent nuclear migration through association with \\u03b1-tubulin and dynactin [#17, #18, #19].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established that the UBL4A ortholog is a UBL-domain protein lacking canonical ubiquitin processing and is needed for cytoskeletal organization, answering whether this UBL behaves like ubiquitin or has a distinct cellular role.\",\n      \"evidence\": \"Yeast mdy2\\u0394 deletion phenotyping, His-tag processing assay, and microtubule/Kar9 immunofluorescence\",\n      \"pmids\": [\"16390866\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis linking Mdy2 to microtubule/Kar9 localization not defined\", \"Relevance to mammalian UBL4A function untested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identified the Sgt2 N-terminus and the chaperone Ydj1 as physical partners of the ortholog, placing it within a chaperone-adaptor network rather than acting alone.\",\n      \"evidence\": \"Co-immunoprecipitation and genetic interaction assays in yeast\",\n      \"pmids\": [\"17441508\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. bridged nature of the Ydj1 association unresolved\", \"Structural interface undefined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Positioned Get4/Get5 upstream of Get3 in the TA-targeting pathway by showing nucleotide-dependent Get3 binding to a conserved Get4 surface, defining the pathway's directional architecture.\",\n      \"evidence\": \"Crystal structure of the Get4/Get5 N-terminal fragment with ITC and co-IP\",\n      \"pmids\": [\"20554915\", \"20106980\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How substrate is handed from Get5/Sgt2 to Get3 not yet resolved at this stage\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Linked the ortholog to cytoskeletal and stress-granule machinery, showing it associates with \\u03b1-tubulin and dynactin and relocalizes to stress granules under heat, expanding its role beyond TA targeting.\",\n      \"evidence\": \"Co-precipitation and GFP live imaging with stress-granule markers in yeast\",\n      \"pmids\": [\"20722039\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of tubulin/dynactin binding unclear\", \"Whether mammalian UBL4A shares these contacts untested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Distinguished cooperative from independent roles of Sgt2 and Get5, showing they act together in TA sorting yet Sgt2 retains a Get5-independent delivery function to Get3.\",\n      \"evidence\": \"Genetic epistasis of sgt2\\u0394 get5\\u0394 double mutants and overexpression toxicity assays\",\n      \"pmids\": [\"21619481\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Biochemical basis of the Get5-independent route not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the molecular handshake of the pathway: the noncanonical SGTA UBD engages the unconventional UBL4A UBL domain via electrostatics, recruiting SGTA to BAG6 and preventing aggregate formation during ERAD.\",\n      \"evidence\": \"NMR, crystal structures (yeast and human), ITC, chemical shift perturbation, and co-IP across two studies\",\n      \"pmids\": [\"23246001\", \"23142665\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate transfer dynamics across the interface not directly visualized\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Established NLS-dependent nuclear import as a prerequisite for the ortholog's heat-stress response and Pab1 interaction, revealing a nuclear-history requirement for its stress function.\",\n      \"evidence\": \"NLS/NES deletion mutants, GFP localization, co-precipitation with Pab1, and heat-stress viability in yeast\",\n      \"pmids\": [\"23285234\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Why nuclear transit is required for cytoplasmic stress-granule function is unexplained\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the binding stoichiometry and atomic interface (1 Sgt2 dimer : 1 Get5 UBL) and validated the contact residues, providing structural ground truth for the SGTA-UBL4A complex.\",\n      \"evidence\": \"NMR solution structure, crystal structure, ITC, and site-directed mutagenesis\",\n      \"pmids\": [\"23297211\", \"24100326\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational changes during substrate loading not captured\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended UBL4A into the DNA-damage response, showing nuclear translocation with BAG6/GET4 and a requirement for BRCA1 recruitment and damage-induced cell death.\",\n      \"evidence\": \"siRNA knockdown, viability assays, immunofluorescence, and BRCA1 recruitment assays\",\n      \"pmids\": [\"23723067\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanistic link between the complex and BRCA1 recruitment undefined\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed how the pathway is kinetically regulated: Get4 primes Get3 in an ATP-bound ternary complex to optimize TA-substrate capture, defining the catalytic logic of targeting.\",\n      \"evidence\": \"Crystal structure of the Get3-Get4-Get5 ternary complex with ATPase and structure-guided assays\",\n      \"pmids\": [\"24727835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full hand-off to the ER membrane downstream of Get3 not captured in this complex\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated that UBL4A and BAG6 UBL domains compete for the same SGTA site, establishing a regulatory switch at the SGTA dimerization domain.\",\n      \"evidence\": \"NMR structure, ITC, microscale thermophoresis, and HADDOCK docking\",\n      \"pmids\": [\"25415308\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger that selects UBL4A vs. BAG6 occupancy unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined the BAG6-UBL4A heterodimerization through a novel C-terminal BAGS interface and showed BAG6 binding stabilizes UBL4A, explaining co-dependence of complex members.\",\n      \"evidence\": \"Crystal structure with biochemical and cell-based stability assays\",\n      \"pmids\": [\"25713138\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How stability control feeds back on TA-targeting flux not addressed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Opened a TA-independent role by showing UBL4A directly binds Arp2/3 to accelerate actin branching, enabling insulin-induced Akt membrane translocation and glycogen synthesis.\",\n      \"evidence\": \"In vitro actin branching, interaction assays, Ubl4A KO mouse, and live-cell Akt imaging\",\n      \"pmids\": [\"26195787\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the UBL and Arp2/3-binding functions are spatially partitioned in cells unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Generalized the actin role to motility, showing UBL4A loss impairs membrane protrusion, fibroblast and macrophage migration, and wound healing.\",\n      \"evidence\": \"Ubl4A KO mouse, wound-healing, ex vivo migration, and motility assays\",\n      \"pmids\": [\"27998771\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct dependence on Arp2/3 binding not tested with domain mutants here\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mapped the Arp2/3 contact to the UBL4A C-terminus and identified D122 as the critical residue whose mutation abolishes binding, destabilizes the protein, and removes pro-death activity in colon cancer.\",\n      \"evidence\": \"In vitro pull-down, D122A mutagenesis, and cell death assays\",\n      \"pmids\": [\"30146258\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of D122-mediated Arp2/3 contact not solved\", \"Single-study finding\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Assigned UBL4A an immune-signaling role by trapping TC45/PTPN2 to disrupt the phosphatase complex that dephosphorylates p65, sustaining NF-\\u03baB activation.\",\n      \"evidence\": \"Reciprocal co-IP, luciferase reporters, and tissue-specific KO mice in LPS and DSS colitis models\",\n      \"pmids\": [\"30867837\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether this competes with TA-targeting functions of UBL4A unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended immune function to antiviral signaling, showing UBL4A binds TRAF6 and promotes its K63-linked ubiquitination to amplify type I IFN responses.\",\n      \"evidence\": \"Co-IP, K63-specific ubiquitination assays, knockdown/overexpression, and phosphorylation blots\",\n      \"pmids\": [\"31451677\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether UBL4A acts as or recruits the E3 ligase for TRAF6 not determined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linked UBL4A to lysosomal control by showing direct LAMP1 interaction that impairs lysosomal function and autophagic degradation in pancreatic cancer.\",\n      \"evidence\": \"Co-IP, autophagy marker blots, and in vitro/orthotopic functional rescue\",\n      \"pmids\": [\"31288830\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP method for direct interaction without reciprocal structural validation\", \"Mechanism of LAMP1-mediated lysosomal impairment unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Tied the Arp2/3 axis to mitochondrial homeostasis, showing UBL4A promotes nutrient-stress mitochondrial fusion and that an Arp2/3-binding-deficient mutant fails to rescue fragmentation and apoptosis.\",\n      \"evidence\": \"Ubl4A KO cells with WT vs. Arp2/3-binding mutant rescue, mitochondrial imaging, ROS, and caspase-9 assays\",\n      \"pmids\": [\"33211772\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How perimitochondrial primed Arp2/3 drives fusion mechanically not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed that the BAG6-UBL4A complex is disrupted by proteotoxic stress, connecting complex integrity to impaired TA biogenesis under disease-relevant conditions.\",\n      \"evidence\": \"Co-IP under polyglutamine, proteasome inhibition, and mitochondrial depolarization\",\n      \"pmids\": [\"37747814\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence on TA-protein flux measured indirectly\", \"Single-study finding\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proposed a UBL4A-STAT3 axis in which UBL4A reduces STAT3 phosphorylation and downstream oncogenic target expression in breast cancer.\",\n      \"evidence\": \"Dual-luciferase reporter, immunofluorescence colocalization, phosphorylation blots, and KO mouse tumor model\",\n      \"pmids\": [\"39487760\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct binding assay (co-IP/pull-down) reported for the UBL4A-STAT3 interaction\", \"Single-lab study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBL4A partitions among its multiple roles—TA-protein holdase, Arp2/3-driven actin scaffold, immune signaling regulator, and nuclear damage-response factor—and what governs the switch between them remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model coordinating cytosolic, immune, and nuclear functions\", \"Structural basis of the C-terminal Arp2/3 contact unsolved\", \"Triggers selecting BAG6 vs. SGTA vs. non-canonical partners unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [8, 10, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 2, 8]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7, 19]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 5, 15]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [11, 12]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"complexes\": [\n      \"BAG6-UBL4A-TRC35/GET4 holdase complex\",\n      \"Get3-Get4-Get5 targeting complex\"\n    ],\n    \"partners\": [\n      \"SGTA\",\n      \"BAG6\",\n      \"GET4\",\n      \"GET3\",\n      \"ARPC (Arp2/3 complex)\",\n      \"TRAF6\",\n      \"PTPN2\",\n      \"LAMP1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}