{"gene":"UBE2E1","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":1996,"finding":"UbcH6 (UBE2E1) interacts with the HECT domain E3 ligase E6-AP and can participate in E6-AP-dependent ubiquitination, though with weak activity compared to UbcH5; UbcH6 does not efficiently interact with the HECT protein RSP5, demonstrating selectivity among HECT E3 partners.","method":"In vitro ubiquitination assay, protein-protein interaction assays (pulldown/binding)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution of ubiquitination with multiple E2/E3 combinations, replicated across HECT partners","pmids":["8576257"],"is_preprint":false},{"year":2005,"finding":"UbcH6 (UBE2E1) is covalently modified by ISG15 at Lys136 (near the catalytic Cys131), forming a thioester intermediate with ISG15. ISG15 conjugation to UbcH6 suppresses its ubiquitin E2 enzyme activity, providing a regulatory link between the ISG15 and ubiquitin conjugation systems.","method":"In vitro ISGylation assay, site-directed mutagenesis, thioester intermediate detection, biochemical fractionation of modified vs. unmodified UbcH6","journal":"Journal of biochemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with mutagenesis identifying catalytic and conjugation sites, multiple orthogonal methods","pmids":["16428300"],"is_preprint":false},{"year":2006,"finding":"UbcH6 (UBE2E1) functions as the E2 for the novel RING E3 ligase RING105 to ubiquitinate TSSC5, with the polyubiquitin target site on TSSC5 mapped to its 6th hydrophilic loop.","method":"In vitro ubiquitination assay, co-immunoprecipitation, mutant RING105 controls, cellular overexpression with cell cycle readout","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro ubiquitination reconstitution plus active-site mutant controls and cellular phenotype","pmids":["16314844"],"is_preprint":false},{"year":2008,"finding":"UbcH6 (UBE2E1) interacts with and ubiquitinates ataxin-1 (SCA1 gene product) in an E3-independent manner, interacting via the ataxin-1 AXH domain; UbcH6 expression regulates the rate of ataxin-1 proteasomal degradation and its nuclear co-localization.","method":"Yeast two-hybrid screen, co-immunoprecipitation, co-localization (confocal microscopy), in vitro ubiquitination assay, domain mapping","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods including reciprocal Co-IP, in vitro ubiquitination, and localization, but single lab","pmids":["18439907"],"is_preprint":false},{"year":2008,"finding":"UbcH6 (UBE2E1) modulates the transcriptional repression activity of ataxin-1 by promoting its degradation; overexpression of UbcH6 reduces ataxin-1 transcriptional repression and aggregate formation, with differential effects depending on polyglutamine tract length (30Q vs 82Q).","method":"Transcriptional repression assay, protein half-life measurement, shRNA knockdown, aggregate formation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — functional cellular assays with KD/OE and specific transcriptional readout, single lab","pmids":["18519031"],"is_preprint":false},{"year":2013,"finding":"USP7 forms a complex with UBE2E1 via the ASTS motif in the unique N-terminal extension of UBE2E1, attenuates UBE2E1-mediated ubiquitination in a manner requiring USP7 catalytic activity and the UBE2E1 N-terminal ASTS sequence, and maintains steady-state UBE2E1 protein levels in cells.","method":"Co-immunoprecipitation (in vitro and in vivo), in vitro ubiquitination assay, USP7 catalytic mutant controls, knockdown/overexpression cellular assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro and in vivo binding, reconstituted ubiquitination assay, mutagenesis, multiple orthogonal methods","pmids":["23603909"],"is_preprint":false},{"year":2017,"finding":"UBE2E1 is a critical in vivo E2 for the PRC1 E3 ligase complex-mediated monoubiquitination of histone H2A at Lys-119 (uH2AK119); UBE2E1 physically interacts with PRC1 subunits Ring1A and Ring1B; catalytically inactive UBE2E1_C131A or UBE2E1 knockdown reduces uH2AK119 and alleviates p16INK4a promoter repression. USP7 is also a key regulator of uH2AK119 through its regulation of UBE2E1.","method":"Co-immunoprecipitation, catalytic mutant (C131A), shRNA knockdown, overexpression, chromatin immunoprecipitation (p16INK4a promoter), cell growth assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, catalytic mutant controls, epistasis to USP7, specific histone modification readout","pmids":["28073915"],"is_preprint":false},{"year":2018,"finding":"OTUB1 non-catalytically stabilizes UBE2E1 protein levels by binding UBE2E1 and suppressing its autoubiquitination, thereby preventing UBE2E1 proteasomal degradation; Otub1 knockout mice show late-stage embryonic lethality and dramatic destabilization of UBE2E1.","method":"OTUB1 knockout mouse and cell lines, in vitro ubiquitination/autoubiquitination assay, catalytic mutant OTUB1 controls, protein stability assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — knockout mouse model, in vitro reconstitution, catalytic vs. binding mutant distinction, orthogonal in vivo and in vitro evidence","pmids":["30282802"],"is_preprint":false},{"year":2018,"finding":"UBE2E1 (E2E1) expression is restricted to slow-twitch (type I and IIA) muscle fibers; knockdown of UBE2E1 exacerbates muscle atrophy under dexamethasone-induced catabolic conditions in both C2C12 myotubes and mouse tibialis anterior muscle, indicating a protective role in muscle mass maintenance.","method":"Immunofluorescence fiber-type localization, shRNA knockdown in vitro and in vivo, dexamethasone atrophy model, muscle mass/protein content measurement","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization with fiber-type specificity, in vivo KD with defined phenotype, but limited mechanistic pathway detail","pmids":["30453501"],"is_preprint":false},{"year":2019,"finding":"Crystal structure (2.82 Å) of the TRIM21 RING domain in complex with UBE2E1 captured a TRIM21 substrate lysine in the UBE2E1 active site, revealing that substrate lysine entry direction is similar to PCNA ubiquitination and differs from canonical SUMO-targeted substrate entry; coordination of the acceptor lysine remodels interactions at the UBE2E1 active site including the conserved RING E3 'linchpin' residue, suggesting an allosteric activation mechanism.","method":"X-ray crystallography (2.82 Å), in vitro ubiquitination assay, mutagenesis of active-site residues, small-angle X-ray scattering","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional mutagenesis validation and in vitro ubiquitination reconstitution","pmids":["31160341"],"is_preprint":false},{"year":2022,"finding":"UBE2E1 polyubiquitinates β-catenin and physically interacts with the ciliopathy protein MKS1 and E3 ligase RNF34; UBE2E1 and MKS1 co-localize at the ciliary base, UBE2E1 levels are co-dependent with MKS1, and UBE2E1 mediates both regulatory and degradative ubiquitination of MKS1; loss of UBE2E1 recapitulates ciliary and Wnt signaling phenotypes of MKS1 loss.","method":"Co-immunoprecipitation, co-localization (confocal microscopy), siRNA knockdown, in vitro ubiquitination assay, Wnt signaling reporter assay, mouse model (Mks1 knockout)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, colocalization, in vitro ubiquitination, in vivo mouse model), epistasis analysis placing UBE2E1 in ciliary Wnt pathway","pmids":["35170427"],"is_preprint":false},{"year":2024,"finding":"UBE2E1 can perform E3-independent substrate ubiquitination through a peptide sequence-dependent mechanism; crystal structure of UBE2E1 in complex with a SETDB1-derived peptide revealed the structural basis for substrate sequence recognition in the UBE2E1 active site, enabling development of an E3-free enzymatic ubiquitination strategy (SUE1).","method":"X-ray crystallography of UBE2E1-substrate peptide complex, in vitro ubiquitination assay (E3-free), mutagenesis, chemical protein synthesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional in vitro reconstitution and mutagenesis validating the mechanism","pmids":["38341401"],"is_preprint":false}],"current_model":"UBE2E1 (UbcH6) is a ubiquitin-conjugating E2 enzyme with a unique N-terminal extension that enables regulation by USP7 (via ASTS motif binding) and OTUB1 (which non-catalytically prevents UBE2E1 autoubiquitination and proteasomal degradation); it functions with HECT E3s (E6-AP), RING E3s (TRIM21, RING105, PRC1/Ring1A/Ring1B, RNF34), and also independently of E3 ligases to ubiquitinate substrates including histone H2A at Lys-119, β-catenin, ataxin-1, TSSC5, MKS1, and SETDB1 via a peptide sequence-dependent active-site mechanism; its activity is negatively regulated by ISG15 conjugation at Lys136, and it plays roles in Polycomb-mediated gene silencing, ciliary Wnt/β-catenin signaling, neurodegenerative disease protein homeostasis, and skeletal muscle mass maintenance."},"narrative":{"teleology":[{"year":1996,"claim":"Establishing UBE2E1 as a functional ubiquitin-conjugating enzyme with selective E3 partnerships resolved its enzymatic identity: UBE2E1 cooperates with the HECT E3 E6-AP but not RSP5, indicating intrinsic selectivity among E3 partners.","evidence":"In vitro ubiquitination reconstitution with multiple E2/E3 combinations and protein-protein interaction assays","pmids":["8576257"],"confidence":"High","gaps":["Range of physiological E3 partners unknown","No cellular substrates identified","No structural basis for E3 selectivity"]},{"year":2005,"claim":"Demonstrating that ISG15 conjugation at Lys136 suppresses UBE2E1 ubiquitin E2 activity revealed a regulatory crosstalk mechanism between the ISG15 and ubiquitin conjugation systems.","evidence":"In vitro ISGylation assay with site-directed mutagenesis and thioester intermediate detection","pmids":["16428300"],"confidence":"High","gaps":["Physiological contexts in which ISGylation regulates UBE2E1 not defined","Effect of ISGylation on specific substrate ubiquitination not tested"]},{"year":2006,"claim":"Identifying UBE2E1 as the E2 for the RING E3 RING105 in ubiquitinating TSSC5 established UBE2E1 function with RING-type E3 ligases and linked it to cell cycle regulation.","evidence":"In vitro ubiquitination reconstitution with RING105 active-site mutant controls and cellular overexpression","pmids":["16314844"],"confidence":"High","gaps":["Endogenous RING105–UBE2E1 complex not validated","TSSC5 ubiquitination sites not mapped"]},{"year":2008,"claim":"Showing that UBE2E1 ubiquitinates ataxin-1 independently of an E3 ligase and regulates its proteasomal degradation and aggregate formation established a direct role in neurodegenerative protein homeostasis.","evidence":"Yeast two-hybrid, reciprocal Co-IP, in vitro E3-free ubiquitination, and transcriptional repression/aggregate assays in mammalian cells","pmids":["18439907","18519031"],"confidence":"Medium","gaps":["In vivo relevance in SCA1 mouse models not tested","Mechanism of E3-independent substrate recognition unknown at this point","Single laboratory findings"]},{"year":2013,"claim":"Identifying USP7 as a binding partner and regulator of UBE2E1 through the N-terminal ASTS motif revealed a deubiquitinase-dependent mechanism that maintains UBE2E1 protein levels and attenuates its ubiquitination activity.","evidence":"In vitro and in vivo Co-IP, reconstituted ubiquitination with USP7 catalytic mutants, knockdown/overexpression cellular assays","pmids":["23603909"],"confidence":"High","gaps":["Structural basis of ASTS motif recognition by USP7 not resolved","Whether USP7 regulation is constitutive or signal-dependent unknown"]},{"year":2017,"claim":"Demonstrating that UBE2E1 is a critical E2 for PRC1-mediated histone H2A Lys-119 monoubiquitination placed UBE2E1 in Polycomb-mediated transcriptional repression and connected USP7 regulation of UBE2E1 to epigenetic gene silencing.","evidence":"Co-IP with Ring1A/Ring1B, C131A catalytic mutant, shRNA knockdown, ChIP at p16INK4a promoter","pmids":["28073915"],"confidence":"High","gaps":["Whether UBE2E1 is the sole or dominant E2 for PRC1 in all cell types not established","Genome-wide H2AK119ub changes upon UBE2E1 loss not profiled"]},{"year":2018,"claim":"Establishing that OTUB1 non-catalytically stabilizes UBE2E1 by blocking autoubiquitination—with Otub1 knockout mice showing embryonic lethality and UBE2E1 destabilization—defined a second deubiquitinase-dependent regulatory axis for UBE2E1 protein homeostasis.","evidence":"Otub1 knockout mouse and cell lines, in vitro autoubiquitination assay, catalytic vs. binding mutant controls","pmids":["30282802"],"confidence":"High","gaps":["Relative contribution of UBE2E1 destabilization to Otub1 knockout lethality not isolated","Other E2 enzymes stabilized by OTUB1 not fully surveyed"]},{"year":2018,"claim":"Localizing UBE2E1 to slow-twitch muscle fibers and showing that its knockdown exacerbates dexamethasone-induced atrophy revealed a tissue-specific protective role in skeletal muscle mass maintenance.","evidence":"Fiber-type immunofluorescence, shRNA knockdown in C2C12 myotubes and mouse tibialis anterior, dexamethasone atrophy model","pmids":["30453501"],"confidence":"Medium","gaps":["UBE2E1 substrates mediating muscle protection not identified","Fiber-type restriction mechanism unknown","Single study without genetic knockout validation"]},{"year":2019,"claim":"Solving the crystal structure of the TRIM21 RING–UBE2E1 complex with a substrate lysine captured in the active site revealed the allosteric activation mechanism and showed that substrate lysine entry differs from canonical SUMO-targeted ubiquitination.","evidence":"X-ray crystallography at 2.82 Å, active-site mutagenesis, in vitro ubiquitination reconstitution, SAXS","pmids":["31160341"],"confidence":"High","gaps":["How E3-independent substrate recognition compares structurally was unresolved","Dynamics of allosteric activation not captured"]},{"year":2022,"claim":"Placing UBE2E1 at the ciliary base in complex with MKS1 and RNF34, where it polyubiquitinates β-catenin and controls MKS1 stability, established UBE2E1 as a regulator of ciliary Wnt/β-catenin signaling.","evidence":"Co-IP, colocalization, siRNA knockdown, in vitro ubiquitination, Wnt reporter assay, Mks1 knockout mouse epistasis","pmids":["35170427"],"confidence":"High","gaps":["Whether UBE2E1 directly ubiquitinates β-catenin at cilia or acts through MKS1 not fully dissected","Ciliopathy patient mutations in UBE2E1 not reported"]},{"year":2024,"claim":"Solving the crystal structure of UBE2E1 bound to a SETDB1-derived substrate peptide revealed that UBE2E1 performs E3-independent ubiquitination through peptide-sequence-dependent active-site recognition, providing a structural basis for its unusual E3-free activity.","evidence":"X-ray crystallography of UBE2E1–peptide complex, E3-free in vitro ubiquitination, mutagenesis, chemical protein synthesis","pmids":["38341401"],"confidence":"High","gaps":["Scope of endogenous substrates recognized by this E3-free mechanism unknown","Whether E3-independent activity is regulated in vivo not addressed"]},{"year":null,"claim":"It remains unknown how UBE2E1's E3-dependent and E3-independent activities are partitioned among its diverse substrates in vivo, what signals dictate the choice between mono- and polyubiquitination, and whether UBE2E1 contributes to human ciliopathy or neurodegenerative disease.","evidence":"","pmids":[],"confidence":"High","gaps":["Systematic identification of endogenous UBE2E1 substrates lacking","Chain-type specificity (K48 vs K63 vs monoubiquitin) across different E3 partnerships not comprehensively defined","No human disease-causing mutations reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,6,9,10,11]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,3,6,10,11]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,6]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[10]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,3,6,7,10,11]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[6]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10]}],"complexes":["PRC1 (Ring1A/Ring1B)"],"partners":["USP7","OTUB1","TRIM21","RING1B","RING1A","MKS1","RNF34","E6AP"],"other_free_text":[]},"mechanistic_narrative":"UBE2E1 (UbcH6) is a ubiquitin-conjugating E2 enzyme that functions with diverse RING and HECT E3 ligases—and also independently of E3 ligases—to ubiquitinate substrates including histone H2A at Lys-119, β-catenin, ataxin-1, TSSC5, MKS1, and SETDB1, thereby participating in Polycomb-mediated gene silencing, ciliary Wnt/β-catenin signaling, and protein homeostasis [PMID:28073915, PMID:35170427, PMID:18439907, PMID:38341401]. Its unique N-terminal extension contains an ASTS motif that mediates binding to the deubiquitinase USP7, which stabilizes UBE2E1 levels and modulates its ubiquitination output, while OTUB1 non-catalytically prevents UBE2E1 autoubiquitination and proteasomal degradation [PMID:23603909, PMID:30282802]. UBE2E1 activity is negatively regulated by ISG15 conjugation at Lys136 near its catalytic cysteine, linking the interferon-stimulated ISG15 pathway to ubiquitin conjugation [PMID:16428300]. Structural studies reveal that substrate lysine enters the UBE2E1 active site through a trajectory distinct from canonical SUMO-targeted mechanisms, and that UBE2E1 possesses intrinsic peptide-sequence-dependent substrate recognition enabling E3-independent ubiquitination [PMID:31160341, PMID:38341401]."},"prefetch_data":{"uniprot":{"accession":"P51965","full_name":"Ubiquitin-conjugating enzyme E2 E1","aliases":["(E3-independent) E2 ubiquitin-conjugating enzyme E1","E2 ubiquitin-conjugating enzyme E1","UbcH6","Ubiquitin carrier protein E1","Ubiquitin-protein ligase E1"],"length_aa":193,"mass_kda":21.4,"function":"Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination. Catalyzes monoubiquitination of other proteins in both an E3-dependent and E3-independent manner (PubMed:27237050)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P51965/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2E1","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UBE2E1","total_profiled":1310},"omim":[{"mim_id":"617233","title":"WD REPEAT-CONTAINING PROTEIN 70; WDR70","url":"https://www.omim.org/entry/617233"},{"mim_id":"617206","title":"NEURALIZED E3 UBIQUITIN PROTEIN LIGASE 3; NEURL3","url":"https://www.omim.org/entry/617206"},{"mim_id":"616017","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 69; TRIM69","url":"https://www.omim.org/entry/616017"},{"mim_id":"616015","title":"RING FINGER PROTEIN 180; RNF180","url":"https://www.omim.org/entry/616015"},{"mim_id":"616014","title":"RING FINGER PROTEIN 25; RNF25","url":"https://www.omim.org/entry/616014"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE2E1"},"hgnc":{"alias_symbol":["UbcH6"],"prev_symbol":[]},"alphafold":{"accession":"P51965","domains":[{"cath_id":"3.10.110.10","chopping":"45-191","consensus_level":"high","plddt":97.1087,"start":45,"end":191}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P51965","model_url":"https://alphafold.ebi.ac.uk/files/AF-P51965-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P51965-F1-predicted_aligned_error_v6.png","plddt_mean":86.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2E1","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2E1"},"sequence":{"accession":"P51965","fasta_url":"https://rest.uniprot.org/uniprotkb/P51965.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P51965/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P51965"}},"corpus_meta":[{"pmid":"8576257","id":"PMC_8576257","title":"Cloning of human ubiquitin-conjugating enzymes UbcH6 and UbcH7 (E2-F1) and characterization of their interaction with E6-AP and RSP5.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8576257","citation_count":137,"is_preprint":false},{"pmid":"16428300","id":"PMC_16428300","title":"Link between the ubiquitin conjugation system and the ISG15 conjugation system: ISG15 conjugation to the UbcH6 ubiquitin E2 enzyme.","date":"2005","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16428300","citation_count":48,"is_preprint":false},{"pmid":"23603909","id":"PMC_23603909","title":"Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23603909","citation_count":41,"is_preprint":false},{"pmid":"16314844","id":"PMC_16314844","title":"Tumor suppressor candidate TSSC5 is regulated by UbcH6 and a novel ubiquitin ligase RING105.","date":"2006","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/16314844","citation_count":39,"is_preprint":false},{"pmid":"30282802","id":"PMC_30282802","title":"OTUB1 non-catalytically stabilizes the E2 ubiquitin-conjugating enzyme UBE2E1 by preventing its autoubiquitination.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30282802","citation_count":36,"is_preprint":false},{"pmid":"31160341","id":"PMC_31160341","title":"E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31160341","citation_count":26,"is_preprint":false},{"pmid":"28073915","id":"PMC_28073915","title":"UbE2E1/UBCH6 Is a Critical in Vivo E2 for the PRC1-catalyzed Ubiquitination of H2A at Lys-119.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28073915","citation_count":24,"is_preprint":false},{"pmid":"38341401","id":"PMC_38341401","title":"Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38341401","citation_count":22,"is_preprint":false},{"pmid":"18439907","id":"PMC_18439907","title":"UbcH6 interacts with and ubiquitinates the SCA1 gene product ataxin-1.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18439907","citation_count":19,"is_preprint":false},{"pmid":"18519031","id":"PMC_18519031","title":"The ubiquitin-conjugating enzyme UbcH6 regulates the transcriptional repression activity of the SCA1 gene product ataxin-1.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18519031","citation_count":13,"is_preprint":false},{"pmid":"35170427","id":"PMC_35170427","title":"Regulation of canonical Wnt signalling by the ciliopathy protein MKS1 and the E2 ubiquitin-conjugating enzyme UBE2E1.","date":"2022","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/35170427","citation_count":12,"is_preprint":false},{"pmid":"30453501","id":"PMC_30453501","title":"UBE2E1 Is Preferentially Expressed in the Cytoplasm of Slow-Twitch Fibers and Protects Skeletal Muscles from Exacerbated Atrophy upon Dexamethasone Treatment.","date":"2018","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/30453501","citation_count":11,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7327,"output_tokens":3311,"usd":0.035823},"stage2":{"model":"claude-opus-4-6","input_tokens":6674,"output_tokens":3128,"usd":0.167355},"total_usd":0.203178,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"UbcH6 (UBE2E1) interacts with the HECT domain E3 ligase E6-AP and can participate in E6-AP-dependent ubiquitination, though with weak activity compared to UbcH5; UbcH6 does not efficiently interact with the HECT protein RSP5, demonstrating selectivity among HECT E3 partners.\",\n      \"method\": \"In vitro ubiquitination assay, protein-protein interaction assays (pulldown/binding)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution of ubiquitination with multiple E2/E3 combinations, replicated across HECT partners\",\n      \"pmids\": [\"8576257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"UbcH6 (UBE2E1) is covalently modified by ISG15 at Lys136 (near the catalytic Cys131), forming a thioester intermediate with ISG15. ISG15 conjugation to UbcH6 suppresses its ubiquitin E2 enzyme activity, providing a regulatory link between the ISG15 and ubiquitin conjugation systems.\",\n      \"method\": \"In vitro ISGylation assay, site-directed mutagenesis, thioester intermediate detection, biochemical fractionation of modified vs. unmodified UbcH6\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with mutagenesis identifying catalytic and conjugation sites, multiple orthogonal methods\",\n      \"pmids\": [\"16428300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"UbcH6 (UBE2E1) functions as the E2 for the novel RING E3 ligase RING105 to ubiquitinate TSSC5, with the polyubiquitin target site on TSSC5 mapped to its 6th hydrophilic loop.\",\n      \"method\": \"In vitro ubiquitination assay, co-immunoprecipitation, mutant RING105 controls, cellular overexpression with cell cycle readout\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro ubiquitination reconstitution plus active-site mutant controls and cellular phenotype\",\n      \"pmids\": [\"16314844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"UbcH6 (UBE2E1) interacts with and ubiquitinates ataxin-1 (SCA1 gene product) in an E3-independent manner, interacting via the ataxin-1 AXH domain; UbcH6 expression regulates the rate of ataxin-1 proteasomal degradation and its nuclear co-localization.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, co-localization (confocal microscopy), in vitro ubiquitination assay, domain mapping\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods including reciprocal Co-IP, in vitro ubiquitination, and localization, but single lab\",\n      \"pmids\": [\"18439907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"UbcH6 (UBE2E1) modulates the transcriptional repression activity of ataxin-1 by promoting its degradation; overexpression of UbcH6 reduces ataxin-1 transcriptional repression and aggregate formation, with differential effects depending on polyglutamine tract length (30Q vs 82Q).\",\n      \"method\": \"Transcriptional repression assay, protein half-life measurement, shRNA knockdown, aggregate formation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional cellular assays with KD/OE and specific transcriptional readout, single lab\",\n      \"pmids\": [\"18519031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"USP7 forms a complex with UBE2E1 via the ASTS motif in the unique N-terminal extension of UBE2E1, attenuates UBE2E1-mediated ubiquitination in a manner requiring USP7 catalytic activity and the UBE2E1 N-terminal ASTS sequence, and maintains steady-state UBE2E1 protein levels in cells.\",\n      \"method\": \"Co-immunoprecipitation (in vitro and in vivo), in vitro ubiquitination assay, USP7 catalytic mutant controls, knockdown/overexpression cellular assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro and in vivo binding, reconstituted ubiquitination assay, mutagenesis, multiple orthogonal methods\",\n      \"pmids\": [\"23603909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"UBE2E1 is a critical in vivo E2 for the PRC1 E3 ligase complex-mediated monoubiquitination of histone H2A at Lys-119 (uH2AK119); UBE2E1 physically interacts with PRC1 subunits Ring1A and Ring1B; catalytically inactive UBE2E1_C131A or UBE2E1 knockdown reduces uH2AK119 and alleviates p16INK4a promoter repression. USP7 is also a key regulator of uH2AK119 through its regulation of UBE2E1.\",\n      \"method\": \"Co-immunoprecipitation, catalytic mutant (C131A), shRNA knockdown, overexpression, chromatin immunoprecipitation (p16INK4a promoter), cell growth assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, catalytic mutant controls, epistasis to USP7, specific histone modification readout\",\n      \"pmids\": [\"28073915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"OTUB1 non-catalytically stabilizes UBE2E1 protein levels by binding UBE2E1 and suppressing its autoubiquitination, thereby preventing UBE2E1 proteasomal degradation; Otub1 knockout mice show late-stage embryonic lethality and dramatic destabilization of UBE2E1.\",\n      \"method\": \"OTUB1 knockout mouse and cell lines, in vitro ubiquitination/autoubiquitination assay, catalytic mutant OTUB1 controls, protein stability assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — knockout mouse model, in vitro reconstitution, catalytic vs. binding mutant distinction, orthogonal in vivo and in vitro evidence\",\n      \"pmids\": [\"30282802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"UBE2E1 (E2E1) expression is restricted to slow-twitch (type I and IIA) muscle fibers; knockdown of UBE2E1 exacerbates muscle atrophy under dexamethasone-induced catabolic conditions in both C2C12 myotubes and mouse tibialis anterior muscle, indicating a protective role in muscle mass maintenance.\",\n      \"method\": \"Immunofluorescence fiber-type localization, shRNA knockdown in vitro and in vivo, dexamethasone atrophy model, muscle mass/protein content measurement\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization with fiber-type specificity, in vivo KD with defined phenotype, but limited mechanistic pathway detail\",\n      \"pmids\": [\"30453501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Crystal structure (2.82 Å) of the TRIM21 RING domain in complex with UBE2E1 captured a TRIM21 substrate lysine in the UBE2E1 active site, revealing that substrate lysine entry direction is similar to PCNA ubiquitination and differs from canonical SUMO-targeted substrate entry; coordination of the acceptor lysine remodels interactions at the UBE2E1 active site including the conserved RING E3 'linchpin' residue, suggesting an allosteric activation mechanism.\",\n      \"method\": \"X-ray crystallography (2.82 Å), in vitro ubiquitination assay, mutagenesis of active-site residues, small-angle X-ray scattering\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional mutagenesis validation and in vitro ubiquitination reconstitution\",\n      \"pmids\": [\"31160341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"UBE2E1 polyubiquitinates β-catenin and physically interacts with the ciliopathy protein MKS1 and E3 ligase RNF34; UBE2E1 and MKS1 co-localize at the ciliary base, UBE2E1 levels are co-dependent with MKS1, and UBE2E1 mediates both regulatory and degradative ubiquitination of MKS1; loss of UBE2E1 recapitulates ciliary and Wnt signaling phenotypes of MKS1 loss.\",\n      \"method\": \"Co-immunoprecipitation, co-localization (confocal microscopy), siRNA knockdown, in vitro ubiquitination assay, Wnt signaling reporter assay, mouse model (Mks1 knockout)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, colocalization, in vitro ubiquitination, in vivo mouse model), epistasis analysis placing UBE2E1 in ciliary Wnt pathway\",\n      \"pmids\": [\"35170427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UBE2E1 can perform E3-independent substrate ubiquitination through a peptide sequence-dependent mechanism; crystal structure of UBE2E1 in complex with a SETDB1-derived peptide revealed the structural basis for substrate sequence recognition in the UBE2E1 active site, enabling development of an E3-free enzymatic ubiquitination strategy (SUE1).\",\n      \"method\": \"X-ray crystallography of UBE2E1-substrate peptide complex, in vitro ubiquitination assay (E3-free), mutagenesis, chemical protein synthesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional in vitro reconstitution and mutagenesis validating the mechanism\",\n      \"pmids\": [\"38341401\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2E1 (UbcH6) is a ubiquitin-conjugating E2 enzyme with a unique N-terminal extension that enables regulation by USP7 (via ASTS motif binding) and OTUB1 (which non-catalytically prevents UBE2E1 autoubiquitination and proteasomal degradation); it functions with HECT E3s (E6-AP), RING E3s (TRIM21, RING105, PRC1/Ring1A/Ring1B, RNF34), and also independently of E3 ligases to ubiquitinate substrates including histone H2A at Lys-119, β-catenin, ataxin-1, TSSC5, MKS1, and SETDB1 via a peptide sequence-dependent active-site mechanism; its activity is negatively regulated by ISG15 conjugation at Lys136, and it plays roles in Polycomb-mediated gene silencing, ciliary Wnt/β-catenin signaling, neurodegenerative disease protein homeostasis, and skeletal muscle mass maintenance.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"UBE2E1 (UbcH6) is a ubiquitin-conjugating E2 enzyme that functions with diverse RING and HECT E3 ligases—and also independently of E3 ligases—to ubiquitinate substrates including histone H2A at Lys-119, β-catenin, ataxin-1, TSSC5, MKS1, and SETDB1, thereby participating in Polycomb-mediated gene silencing, ciliary Wnt/β-catenin signaling, and protein homeostasis [PMID:28073915, PMID:35170427, PMID:18439907, PMID:38341401]. Its unique N-terminal extension contains an ASTS motif that mediates binding to the deubiquitinase USP7, which stabilizes UBE2E1 levels and modulates its ubiquitination output, while OTUB1 non-catalytically prevents UBE2E1 autoubiquitination and proteasomal degradation [PMID:23603909, PMID:30282802]. UBE2E1 activity is negatively regulated by ISG15 conjugation at Lys136 near its catalytic cysteine, linking the interferon-stimulated ISG15 pathway to ubiquitin conjugation [PMID:16428300]. Structural studies reveal that substrate lysine enters the UBE2E1 active site through a trajectory distinct from canonical SUMO-targeted mechanisms, and that UBE2E1 possesses intrinsic peptide-sequence-dependent substrate recognition enabling E3-independent ubiquitination [PMID:31160341, PMID:38341401].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing UBE2E1 as a functional ubiquitin-conjugating enzyme with selective E3 partnerships resolved its enzymatic identity: UBE2E1 cooperates with the HECT E3 E6-AP but not RSP5, indicating intrinsic selectivity among E3 partners.\",\n      \"evidence\": \"In vitro ubiquitination reconstitution with multiple E2/E3 combinations and protein-protein interaction assays\",\n      \"pmids\": [\"8576257\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Range of physiological E3 partners unknown\", \"No cellular substrates identified\", \"No structural basis for E3 selectivity\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating that ISG15 conjugation at Lys136 suppresses UBE2E1 ubiquitin E2 activity revealed a regulatory crosstalk mechanism between the ISG15 and ubiquitin conjugation systems.\",\n      \"evidence\": \"In vitro ISGylation assay with site-directed mutagenesis and thioester intermediate detection\",\n      \"pmids\": [\"16428300\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological contexts in which ISGylation regulates UBE2E1 not defined\", \"Effect of ISGylation on specific substrate ubiquitination not tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identifying UBE2E1 as the E2 for the RING E3 RING105 in ubiquitinating TSSC5 established UBE2E1 function with RING-type E3 ligases and linked it to cell cycle regulation.\",\n      \"evidence\": \"In vitro ubiquitination reconstitution with RING105 active-site mutant controls and cellular overexpression\",\n      \"pmids\": [\"16314844\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous RING105–UBE2E1 complex not validated\", \"TSSC5 ubiquitination sites not mapped\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showing that UBE2E1 ubiquitinates ataxin-1 independently of an E3 ligase and regulates its proteasomal degradation and aggregate formation established a direct role in neurodegenerative protein homeostasis.\",\n      \"evidence\": \"Yeast two-hybrid, reciprocal Co-IP, in vitro E3-free ubiquitination, and transcriptional repression/aggregate assays in mammalian cells\",\n      \"pmids\": [\"18439907\", \"18519031\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo relevance in SCA1 mouse models not tested\", \"Mechanism of E3-independent substrate recognition unknown at this point\", \"Single laboratory findings\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identifying USP7 as a binding partner and regulator of UBE2E1 through the N-terminal ASTS motif revealed a deubiquitinase-dependent mechanism that maintains UBE2E1 protein levels and attenuates its ubiquitination activity.\",\n      \"evidence\": \"In vitro and in vivo Co-IP, reconstituted ubiquitination with USP7 catalytic mutants, knockdown/overexpression cellular assays\",\n      \"pmids\": [\"23603909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ASTS motif recognition by USP7 not resolved\", \"Whether USP7 regulation is constitutive or signal-dependent unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that UBE2E1 is a critical E2 for PRC1-mediated histone H2A Lys-119 monoubiquitination placed UBE2E1 in Polycomb-mediated transcriptional repression and connected USP7 regulation of UBE2E1 to epigenetic gene silencing.\",\n      \"evidence\": \"Co-IP with Ring1A/Ring1B, C131A catalytic mutant, shRNA knockdown, ChIP at p16INK4a promoter\",\n      \"pmids\": [\"28073915\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether UBE2E1 is the sole or dominant E2 for PRC1 in all cell types not established\", \"Genome-wide H2AK119ub changes upon UBE2E1 loss not profiled\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Establishing that OTUB1 non-catalytically stabilizes UBE2E1 by blocking autoubiquitination—with Otub1 knockout mice showing embryonic lethality and UBE2E1 destabilization—defined a second deubiquitinase-dependent regulatory axis for UBE2E1 protein homeostasis.\",\n      \"evidence\": \"Otub1 knockout mouse and cell lines, in vitro autoubiquitination assay, catalytic vs. binding mutant controls\",\n      \"pmids\": [\"30282802\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of UBE2E1 destabilization to Otub1 knockout lethality not isolated\", \"Other E2 enzymes stabilized by OTUB1 not fully surveyed\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Localizing UBE2E1 to slow-twitch muscle fibers and showing that its knockdown exacerbates dexamethasone-induced atrophy revealed a tissue-specific protective role in skeletal muscle mass maintenance.\",\n      \"evidence\": \"Fiber-type immunofluorescence, shRNA knockdown in C2C12 myotubes and mouse tibialis anterior, dexamethasone atrophy model\",\n      \"pmids\": [\"30453501\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"UBE2E1 substrates mediating muscle protection not identified\", \"Fiber-type restriction mechanism unknown\", \"Single study without genetic knockout validation\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Solving the crystal structure of the TRIM21 RING–UBE2E1 complex with a substrate lysine captured in the active site revealed the allosteric activation mechanism and showed that substrate lysine entry differs from canonical SUMO-targeted ubiquitination.\",\n      \"evidence\": \"X-ray crystallography at 2.82 Å, active-site mutagenesis, in vitro ubiquitination reconstitution, SAXS\",\n      \"pmids\": [\"31160341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How E3-independent substrate recognition compares structurally was unresolved\", \"Dynamics of allosteric activation not captured\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Placing UBE2E1 at the ciliary base in complex with MKS1 and RNF34, where it polyubiquitinates β-catenin and controls MKS1 stability, established UBE2E1 as a regulator of ciliary Wnt/β-catenin signaling.\",\n      \"evidence\": \"Co-IP, colocalization, siRNA knockdown, in vitro ubiquitination, Wnt reporter assay, Mks1 knockout mouse epistasis\",\n      \"pmids\": [\"35170427\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether UBE2E1 directly ubiquitinates β-catenin at cilia or acts through MKS1 not fully dissected\", \"Ciliopathy patient mutations in UBE2E1 not reported\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Solving the crystal structure of UBE2E1 bound to a SETDB1-derived substrate peptide revealed that UBE2E1 performs E3-independent ubiquitination through peptide-sequence-dependent active-site recognition, providing a structural basis for its unusual E3-free activity.\",\n      \"evidence\": \"X-ray crystallography of UBE2E1–peptide complex, E3-free in vitro ubiquitination, mutagenesis, chemical protein synthesis\",\n      \"pmids\": [\"38341401\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Scope of endogenous substrates recognized by this E3-free mechanism unknown\", \"Whether E3-independent activity is regulated in vivo not addressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how UBE2E1's E3-dependent and E3-independent activities are partitioned among its diverse substrates in vivo, what signals dictate the choice between mono- and polyubiquitination, and whether UBE2E1 contributes to human ciliopathy or neurodegenerative disease.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Systematic identification of endogenous UBE2E1 substrates lacking\", \"Chain-type specificity (K48 vs K63 vs monoubiquitin) across different E3 partnerships not comprehensively defined\", \"No human disease-causing mutations reported\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 6, 9, 10, 11]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 3, 6, 10, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 3, 6, 7, 10, 11]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [\n      \"PRC1 (Ring1A/Ring1B)\"\n    ],\n    \"partners\": [\n      \"USP7\",\n      \"OTUB1\",\n      \"TRIM21\",\n      \"Ring1B\",\n      \"Ring1A\",\n      \"MKS1\",\n      \"RNF34\",\n      \"E6AP\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}