{"gene":"SPRYD3","run_date":"2026-06-10T07:46:41","timeline":{"discoveries":[{"year":2025,"finding":"SPRYD3 acts as a substrate specificity factor for the E3 ubiquitin ligase MYCBP2 (PAM), forming an E3 ligase complex (SPRYD3-MYCBP2) distinct from the previously known FBXO45-MYCBP2 complex.","method":"Co-immunoprecipitation and complex identification in cell-based experiments","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complex identification by Co-IP in a single study; single lab but functionally validated with downstream ubiquitination assays","pmids":["41052634"],"is_preprint":false},{"year":2025,"finding":"The SPRYD3-MYCBP2 E3 ligase complex ubiquitinates the deubiquitinase USP11 on cysteine 318 via non-canonical ubiquitination, demonstrating that an E3 ligase and DUB can form a cooperative complex despite opposing enzymatic activities.","method":"Ubiquitination assay with site-specific mutagenesis (USP11 C318) and biochemical complex reconstitution","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro/cell-based ubiquitination assay with mutagenesis identifying specific modification site, single lab with multiple orthogonal methods","pmids":["41052634"],"is_preprint":false},{"year":2025,"finding":"SPRYD3-MYCBP2-mediated ubiquitination of USP11 promotes bipolar spindle formation and facilitates mitotic slippage in the presence of microtubule-targeting drugs, establishing SPRYD3 as a regulator of mitotic cell fate.","method":"Loss-of-function experiments with anti-microtubule drug treatment, spindle assembly assays, and mitotic fate monitoring","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined cellular phenotype (spindle formation, mitotic slippage) linked to specific ubiquitination mechanism; single lab","pmids":["41052634"],"is_preprint":false}],"current_model":"SPRYD3 functions as a substrate specificity factor for the E3 ubiquitin ligase MYCBP2 (PAM), forming a complex that ubiquitinates the deubiquitinase USP11 on cysteine 318 via non-canonical ubiquitination, thereby promoting bipolar spindle formation and mitotic slippage during mitotic arrest caused by anti-microtubule drugs."},"narrative":{"mechanistic_narrative":"SPRYD3 functions as a substrate specificity factor within the ubiquitin–proteasome system that controls mitotic cell fate during anti-microtubule drug-induced arrest [PMID:41052634]. It associates with the E3 ubiquitin ligase MYCBP2 (PAM) to form a SPRYD3-MYCBP2 ligase complex distinct from the previously characterized FBXO45-MYCBP2 complex [PMID:41052634]. This complex ubiquitinates the deubiquitinase USP11 at cysteine 318 through non-canonical ubiquitination, an unusual cooperative arrangement in which an E3 ligase and a DUB act within a single complex [PMID:41052634]. Functionally, SPRYD3-MYCBP2-mediated modification of USP11 promotes bipolar spindle formation and facilitates mitotic slippage in cells treated with microtubule-targeting drugs, establishing SPRYD3 as a regulator of mitotic outcome [PMID:41052634].","teleology":[{"year":2025,"claim":"Establishing whether SPRYD3 has a defined biochemical role, this work identified it as a substrate specificity factor partnering MYCBP2 in a ligase complex separate from the known FBXO45-MYCBP2 assembly.","evidence":"Co-immunoprecipitation and complex identification in cell-based experiments","pmids":["41052634"],"confidence":"Medium","gaps":["Complex identified by Co-IP in a single study without reciprocal structural validation","Stoichiometry and architecture of the SPRYD3-MYCBP2 complex not resolved","Whether SPRYD3 directs MYCBP2 to additional substrates is unknown"]},{"year":2025,"claim":"To define the molecular output of the complex, the substrate and modification site were mapped, showing the SPRYD3-MYCBP2 complex ubiquitinates USP11 on cysteine 318 by non-canonical ubiquitination.","evidence":"Ubiquitination assay with site-specific mutagenesis of USP11 C318 and biochemical complex reconstitution","pmids":["41052634"],"confidence":"High","gaps":["Functional consequence of C318 modification on USP11 catalytic activity not fully resolved","Whether the ubiquitin chain type/linkage is characterized is not stated","Cooperative E3–DUB logic generalizability untested"]},{"year":2025,"claim":"To connect the biochemistry to a cellular phenotype, loss-of-function studies showed the pathway promotes bipolar spindle formation and mitotic slippage under microtubule-targeting drug treatment, placing SPRYD3 as a determinant of mitotic fate.","evidence":"Loss-of-function experiments with anti-microtubule drug treatment, spindle assembly assays, and mitotic fate monitoring","pmids":["41052634"],"confidence":"Medium","gaps":["Single-lab phenotype not independently replicated","Relevance to drug resistance in tumor cells not established","Downstream targets of USP11 mediating spindle effects not identified"]},{"year":null,"claim":"Whether SPRYD3 functions beyond the mitotic MYCBP2-USP11 axis and how it selects substrates structurally remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of SPRYD3 or its substrate-recognition interface","No additional substrates or physiological contexts characterized","Independent confirmation of all findings from a second laboratory absent"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0]}],"localization":[],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[2]}],"complexes":["SPRYD3-MYCBP2 E3 ligase complex"],"partners":["MYCBP2","USP11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NCJ5","full_name":"SPRY domain-containing protein 3","aliases":[],"length_aa":442,"mass_kda":49.7,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q8NCJ5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPRYD3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"MAP4","stoichiometry":0.2},{"gene":"VCP","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SPRYD3","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"},{"location":"Actin filaments","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SPRYD3"},"hgnc":{"alias_symbol":["FLJ14800"],"prev_symbol":[]},"alphafold":{"accession":"Q8NCJ5","domains":[{"cath_id":"2.60.120.920","chopping":"44-197","consensus_level":"high","plddt":94.8876,"start":44,"end":197},{"cath_id":"2.60.120.920","chopping":"219-333_393-435","consensus_level":"high","plddt":93.9659,"start":219,"end":435}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NCJ5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NCJ5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NCJ5-F1-predicted_aligned_error_v6.png","plddt_mean":81.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPRYD3","jax_strain_url":"https://www.jax.org/strain/search?query=SPRYD3"},"sequence":{"accession":"Q8NCJ5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NCJ5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NCJ5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NCJ5"}},"corpus_meta":[{"pmid":"39225086","id":"PMC_39225086","title":"Fkbp5 gene deletion: Circadian rhythm profile and brain proteomics in aged mice.","date":"2024","source":"Aging cell","url":"https://pubmed.ncbi.nlm.nih.gov/39225086","citation_count":9,"is_preprint":false},{"pmid":"38230206","id":"PMC_38230206","title":"NCDN is a Potential Biomarker and Therapeutic Target for Glioblastoma.","date":"2024","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38230206","citation_count":1,"is_preprint":false},{"pmid":"41052634","id":"PMC_41052634","title":"The E3 ubiquitin ligase SPRYD3-MYCBP2(PAM) regulates mitotic cell fate and ubiquitination of USP11 to control spindle assembly.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41052634","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3528,"output_tokens":749,"usd":0.01091,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7164,"output_tokens":1563,"usd":0.037448,"stage2_stop_reason":"end_turn"},"total_usd":0.048358,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"SPRYD3 acts as a substrate specificity factor for the E3 ubiquitin ligase MYCBP2 (PAM), forming an E3 ligase complex (SPRYD3-MYCBP2) distinct from the previously known FBXO45-MYCBP2 complex.\",\n      \"method\": \"Co-immunoprecipitation and complex identification in cell-based experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complex identification by Co-IP in a single study; single lab but functionally validated with downstream ubiquitination assays\",\n      \"pmids\": [\"41052634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The SPRYD3-MYCBP2 E3 ligase complex ubiquitinates the deubiquitinase USP11 on cysteine 318 via non-canonical ubiquitination, demonstrating that an E3 ligase and DUB can form a cooperative complex despite opposing enzymatic activities.\",\n      \"method\": \"Ubiquitination assay with site-specific mutagenesis (USP11 C318) and biochemical complex reconstitution\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro/cell-based ubiquitination assay with mutagenesis identifying specific modification site, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"41052634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SPRYD3-MYCBP2-mediated ubiquitination of USP11 promotes bipolar spindle formation and facilitates mitotic slippage in the presence of microtubule-targeting drugs, establishing SPRYD3 as a regulator of mitotic cell fate.\",\n      \"method\": \"Loss-of-function experiments with anti-microtubule drug treatment, spindle assembly assays, and mitotic fate monitoring\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined cellular phenotype (spindle formation, mitotic slippage) linked to specific ubiquitination mechanism; single lab\",\n      \"pmids\": [\"41052634\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPRYD3 functions as a substrate specificity factor for the E3 ubiquitin ligase MYCBP2 (PAM), forming a complex that ubiquitinates the deubiquitinase USP11 on cysteine 318 via non-canonical ubiquitination, thereby promoting bipolar spindle formation and mitotic slippage during mitotic arrest caused by anti-microtubule drugs.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SPRYD3 functions as a substrate specificity factor within the ubiquitin–proteasome system that controls mitotic cell fate during anti-microtubule drug-induced arrest [#0, #2]. It associates with the E3 ubiquitin ligase MYCBP2 (PAM) to form a SPRYD3-MYCBP2 ligase complex distinct from the previously characterized FBXO45-MYCBP2 complex [#0]. This complex ubiquitinates the deubiquitinase USP11 at cysteine 318 through non-canonical ubiquitination, an unusual cooperative arrangement in which an E3 ligase and a DUB act within a single complex [#1]. Functionally, SPRYD3-MYCBP2-mediated modification of USP11 promotes bipolar spindle formation and facilitates mitotic slippage in cells treated with microtubule-targeting drugs, establishing SPRYD3 as a regulator of mitotic outcome [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"Establishing whether SPRYD3 has a defined biochemical role, this work identified it as a substrate specificity factor partnering MYCBP2 in a ligase complex separate from the known FBXO45-MYCBP2 assembly.\",\n      \"evidence\": \"Co-immunoprecipitation and complex identification in cell-based experiments\",\n      \"pmids\": [\"41052634\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Complex identified by Co-IP in a single study without reciprocal structural validation\",\n        \"Stoichiometry and architecture of the SPRYD3-MYCBP2 complex not resolved\",\n        \"Whether SPRYD3 directs MYCBP2 to additional substrates is unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To define the molecular output of the complex, the substrate and modification site were mapped, showing the SPRYD3-MYCBP2 complex ubiquitinates USP11 on cysteine 318 by non-canonical ubiquitination.\",\n      \"evidence\": \"Ubiquitination assay with site-specific mutagenesis of USP11 C318 and biochemical complex reconstitution\",\n      \"pmids\": [\"41052634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of C318 modification on USP11 catalytic activity not fully resolved\",\n        \"Whether the ubiquitin chain type/linkage is characterized is not stated\",\n        \"Cooperative E3–DUB logic generalizability untested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To connect the biochemistry to a cellular phenotype, loss-of-function studies showed the pathway promotes bipolar spindle formation and mitotic slippage under microtubule-targeting drug treatment, placing SPRYD3 as a determinant of mitotic fate.\",\n      \"evidence\": \"Loss-of-function experiments with anti-microtubule drug treatment, spindle assembly assays, and mitotic fate monitoring\",\n      \"pmids\": [\"41052634\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab phenotype not independently replicated\",\n        \"Relevance to drug resistance in tumor cells not established\",\n        \"Downstream targets of USP11 mediating spindle effects not identified\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether SPRYD3 functions beyond the mitotic MYCBP2-USP11 axis and how it selects substrates structurally remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of SPRYD3 or its substrate-recognition interface\",\n        \"No additional substrates or physiological contexts characterized\",\n        \"Independent confirmation of all findings from a second laboratory absent\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"SPRYD3-MYCBP2 E3 ligase complex\"],\n    \"partners\": [\"MYCBP2\", \"USP11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":4,"faith_pct":75.0}}