{"gene":"ZYG11B","run_date":"2026-04-28T23:00:24","timeline":{"discoveries":[{"year":2004,"finding":"C. elegans ZYG-11 acts as a component of a CUL-2-based E3 ubiquitin ligase that promotes the metaphase-to-anaphase transition at meiosis II by targeting cyclin B (CYB-3) for degradation; inactivation of ZYG-11 leads to CYB-3 accumulation and M phase arrest.","method":"RNAi knockdown in C. elegans, genetic epistasis, cyclin B accumulation assays","journal":"Development","confidence":"High","confidence_rationale":"Tier 2 — replicated in two independent papers using RNAi and genetic analysis, consistent mechanistic conclusion across labs","pmids":["15215208","15215209"],"is_preprint":false},{"year":2004,"finding":"ZYG-11 and CUL-2 regulate embryonic anterior-posterior polarity establishment in C. elegans, with their inactivation causing inverted PAR protein and P granule polarity; this polarity role can operate independently of their cell cycle progression function.","method":"RNAi knockdown, live imaging of PAR proteins and P granules in C. elegans embryos","journal":"Development","confidence":"High","confidence_rationale":"Tier 2 — replicated in two independent papers with consistent epistasis and imaging data","pmids":["15215208","15215209"],"is_preprint":false},{"year":2007,"finding":"ZYG-11 is the substrate-recognition subunit of a CUL-2-based ubiquitin ligase complex; it interacts with CUL-2 in vivo and binds the adaptor protein Elongin C via a nematode variant of the VHL-box motif, establishing ZYG11 family members as conserved CUL2 complex substrate receptors in nematodes and humans.","method":"Co-immunoprecipitation in vivo, VHL-box motif identification, sequence analysis of ZYG11 family across metazoa","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with functional domain identification, conserved across species","pmids":["17304241"],"is_preprint":false},{"year":2021,"finding":"ZYG11B recognizes N-terminal glycine degrons (Gly/N-degrons) via its armadillo (ARM) repeat domain, which forms a deep, narrow cavity engaging the first four residues of the degron; the α-amino group of the glycine is accommodated by five conserved hydrogen bonds in an acidic pocket.","method":"Crystal structure of ZYG11B bound to Gly/N-degron peptides, biochemical binding assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — crystal structures with biochemical validation, multiple Gly/N-degron substrates tested","pmids":["34214466"],"is_preprint":false},{"year":2021,"finding":"SARS-CoV-2 ORF10 interacts with ZYG11B (the substrate receptor of CRL2ZYG11B) through its N-terminus, which is critical for binding; however, ORF10 does not hijack or inhibit CRL2ZYG11B activity and ZYG11B/ZER1 are dispensable for SARS-CoV-2 infection in cultured cells.","method":"Co-immunoprecipitation, N-terminal deletion mapping, ZYG11B/ZER1 knockout cell infection assays, proteomics","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, deletion mapping, KO infection assays) in one study","pmids":["33827988"],"is_preprint":false},{"year":2022,"finding":"ZYG11B (and ZER1) can recognize small N-terminal residues beyond glycine, including Nt-Ser, Nt-Ala, and Nt-Cys in vitro; Nt-acetylation of these residues by N-terminal acetyltransferases (NATs) shields them from ZYG11B recognition, revealing a role for CRL2ZYG11B in Nt-acetylation quality control.","method":"In vitro binding assays, crystal structures of ZYG11B bound to various small Nt-residue peptides, NAT-deficient cell degradation assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — crystal structures combined with in vitro assays and cell-based functional validation","pmids":["36496439"],"is_preprint":false},{"year":2022,"finding":"Crystal structure of ZYG11B bound to the SARS-CoV-2 ORF10 N-terminal peptide reveals the molecular basis for ORF10 recognition by the ARM repeat domain of ZYG11B, consistent with Gly/N-degron recognition mechanism.","method":"Crystal structure determination of ZYG11B–ORF10 peptide complex","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with structural analysis of binding interface","pmids":["35636250"],"is_preprint":false},{"year":2023,"finding":"ZYG11B enhances cGAS-mediated innate immune responses by increasing cGAS-DNA binding affinity, potentiating cGAS-DNA condensation, and stabilizing the cGAS-DNA condensed complex; ZYG11B knockdown impairs cGAMP production and downstream interferon/cytokine transcription. Additionally, HSV-1 infection induces ZYG11B degradation to dampen this response.","method":"ZYG11B knockdown with cGAMP measurement, co-immunoprecipitation, DNA binding affinity assays, condensation assays, HSV-1 infection experiments","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple functional assays in single lab, mechanistic detail shown but not reconstituted in vitro","pmids":["36933219"],"is_preprint":false},{"year":2025,"finding":"ZYG11B targets enterovirus EV71 structural protein VP1 for proteasomal degradation via the CRL2ZYG11B complex, driving K33-linked ubiquitination of VP1; the interaction between ZYG11B and VP1 was confirmed by mass spectrometry and immunoprecipitation, and key domains for VP1 and CUL2 binding were identified.","method":"Mass spectrometry, immunoprecipitation, ubiquitination assays, proteasome inhibition, domain mapping","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple methods (MS, Co-IP, ubiquitination assay) in single lab study","pmids":["40135890"],"is_preprint":false},{"year":2026,"finding":"Cryo-EM structures of full-length human ZYG11B in complex with EloB-EloC adaptor and Gly/N-degron peptide reveal a seahorse-like architecture with distinct interfaces for adaptor binding and substrate engagement; ZYG11B can form both monomeric and dimeric assemblies, with the dimer stabilizing two substrate-binding sites in opposite orientations, and functional assays show all three interfaces (adaptor recruitment, substrate binding, dimerization) are essential for substrate degradation.","method":"Cryo-EM structure determination, functional ubiquitination/degradation assays with interface mutants","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structures of full-length complex combined with mutagenesis and functional degradation assays","pmids":["41917018"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structure of the CRL2-ZYG11B holoenzyme alone and in complex with NLRP1 Gly/N-degron peptide shows ZYG11B folds into an LRR domain followed by two ARM repeat domains that mediate CRL2 assembly and substrate recognition; ZYG11B promotes NLRP1 inflammasome activation by recognizing and ubiquitinating the NLRP1 Gly/N-degron revealed after viral protease cleavage.","method":"Cryo-EM structure determination, in vitro ubiquitination assays, NLRP1 inflammasome activation assays, blocking experiments","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 1 — cryo-EM structures with functional validation, but preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.06.24.600508"],"is_preprint":true},{"year":2020,"finding":"A truncating mutation in human ZYG11B (p.Glu537*) alters subcellular localization of the truncated protein in HeLa cells; morpholino knockdown of zebrafish ZYG11B homologue disrupts craniofacial cartilage architecture and notochord development; ZYG11B expression regulates the cartilage master regulator SOX6 and is regulated by retinoic acid.","method":"Immunofluorescence of mutant ZYG11B in HeLa cells, morpholino knockdown in zebrafish, RT-PCR for SOX6 regulation","journal":"Molecular genetics & genomic medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct localization experiment and in vivo knockdown with defined phenotype, single lab","pmids":["32738032"],"is_preprint":false}],"current_model":"ZYG11B is the substrate-recognition subunit of the CRL2ZYG11B E3 ubiquitin ligase complex, binding EloB/EloC adaptors via a VHL-box motif and engaging substrates through its armadillo (ARM) repeat domain, which forms a deep cavity that specifically recognizes N-terminal glycine (and other small unacetylated N-terminal residues) to drive Gly/N-degron pathway proteasomal degradation; structurally, full-length ZYG11B adopts a seahorse-like architecture that can dimerize to present two substrate-binding sites, and functionally ZYG11B targets cell cycle regulators (cyclin B), viral proteins (EV71 VP1 via K33-linked ubiquitination), and immune sensors (NLRP1 Gly/N-degron after viral protease cleavage), while also enhancing cGAS-DNA condensation to amplify innate immune responses."},"narrative":{"teleology":[{"year":2004,"claim":"Establishing ZYG-11 as a CUL-2-linked cell-cycle regulator answered the question of how meiosis II metaphase-to-anaphase transition is controlled in C. elegans embryos, revealing cyclin B as a degradation target and an additional role in anterior-posterior polarity.","evidence":"RNAi knockdown and genetic epistasis in C. elegans embryos, live imaging of PAR proteins and P granules","pmids":["15215208","15215209"],"confidence":"High","gaps":["Direct biochemical interaction between ZYG-11 and cyclin B not demonstrated","Whether polarity function requires ubiquitin ligase activity or acts through a separate mechanism","Mammalian homolog function unknown"]},{"year":2007,"claim":"Demonstrating that ZYG-11 directly binds CUL-2 and Elongin C via a VHL-box motif established ZYG11 family proteins as bona fide CRL2 substrate-recognition subunits conserved from nematodes to humans.","evidence":"Reciprocal co-immunoprecipitation in vivo, VHL-box motif identification and cross-species sequence analysis","pmids":["17304241"],"confidence":"High","gaps":["No substrate identified for the mammalian ZYG11B paralog","Structural basis of adaptor and substrate engagement unknown"]},{"year":2020,"claim":"A human truncating ZYG11B mutation and zebrafish knockdown linked ZYG11B to craniofacial cartilage and notochord development, revealing a vertebrate developmental function and SOX6 as a downstream regulated gene.","evidence":"Immunofluorescence of mutant protein in HeLa cells, morpholino knockdown in zebrafish, RT-PCR","pmids":["32738032"],"confidence":"Medium","gaps":["Whether SOX6 regulation is direct (i.e., SOX6 is a ubiquitination substrate) or indirect","Single lab, no independent replication of zebrafish phenotype","Mechanism connecting ZYG11B E3 ligase activity to cartilage morphogenesis not defined"]},{"year":2021,"claim":"Crystal structures of ZYG11B bound to Gly/N-degron peptides solved the long-standing question of how the CRL2^ZYG11B complex selects substrates, revealing a narrow ARM-repeat cavity that specifically accommodates the unmodified α-amino group of N-terminal glycine through five conserved hydrogen bonds.","evidence":"Crystal structure determination with multiple Gly/N-degron peptides, biochemical binding assays","pmids":["34214466"],"confidence":"High","gaps":["Whether additional sequence context beyond the first four residues influences substrate selectivity in vivo","Full-length ZYG11B architecture not yet resolved"]},{"year":2021,"claim":"Testing the hypothesis that SARS-CoV-2 ORF10 hijacks CRL2^ZYG11B showed that while ORF10 binds ZYG11B via its N-terminus consistent with Gly/N-degron recognition, it neither co-opts nor inhibits the ligase, and ZYG11B is dispensable for infection.","evidence":"Co-immunoprecipitation, N-terminal deletion mapping, ZYG11B/ZER1 knockout cell infection assays, proteomics","pmids":["33827988"],"confidence":"High","gaps":["Whether ORF10 binding has functional consequences in non-cultured-cell contexts","Whether ORF10 is degraded by CRL2^ZYG11B in vivo"]},{"year":2022,"claim":"Expanding the substrate specificity of ZYG11B beyond glycine to include unacetylated Nt-Ser, Nt-Ala, and Nt-Cys established CRL2^ZYG11B as a quality-control mechanism that degrades proteins escaping N-terminal acetylation.","evidence":"Crystal structures of ZYG11B with various small-residue peptides, in vitro binding assays, NAT-deficient cell degradation assays","pmids":["36496439"],"confidence":"High","gaps":["Endogenous substrates accumulating in NAT-deficient cells due to ZYG11B have not been comprehensively catalogued","Relative contribution of ZYG11B versus ZER1 to Nt-acetylation quality control unclear"]},{"year":2023,"claim":"Demonstrating that ZYG11B enhances cGAS-DNA condensation and cGAMP production revealed an unexpected innate immunity function apparently independent of its canonical E3 ligase role, with HSV-1 degrading ZYG11B as a countermeasure.","evidence":"ZYG11B knockdown, cGAMP measurement, co-immunoprecipitation, DNA binding affinity and condensation assays, HSV-1 infection","pmids":["36933219"],"confidence":"Medium","gaps":["Whether ZYG11B's ubiquitin ligase activity contributes to cGAS regulation not resolved","Mechanism by which HSV-1 targets ZYG11B for degradation not identified","Not independently replicated"]},{"year":2025,"claim":"Identification of enterovirus VP1 as a ZYG11B substrate demonstrated that CRL2^ZYG11B serves as an antiviral E3 ligase mediating K33-linked ubiquitination and proteasomal degradation of a viral structural protein.","evidence":"Mass spectrometry, immunoprecipitation, ubiquitination assays with linkage typing, proteasome inhibition, domain mapping","pmids":["40135890"],"confidence":"Medium","gaps":["Whether VP1 targeting depends on a Gly/N-degron or an alternative recognition mode not clarified","In vivo antiviral significance not tested in animal models","Single lab study"]},{"year":2026,"claim":"Cryo-EM structures of full-length human ZYG11B–EloBC with substrate peptide resolved the overall seahorse-like architecture and revealed functionally essential dimerization, showing that two substrate-binding sites in opposing orientations are required for efficient degradation.","evidence":"Cryo-EM of monomeric and dimeric assemblies, mutagenesis of adaptor, substrate, and dimer interfaces with degradation assays","pmids":["41917018"],"confidence":"High","gaps":["Physiological significance of dimer versus monomer in cells not established","No structure of a full substrate (rather than peptide) bound to the holoenzyme"]},{"year":null,"claim":"Key open questions include the comprehensive identification of endogenous Gly/N-degron substrates in mammalian cells, the functional division of labor between ZYG11B and its paralog ZER1, whether ZYG11B dimerization is regulated, and the molecular mechanism by which ZYG11B enhances cGAS condensation independently of ubiquitination.","evidence":"","pmids":[],"confidence":"Low","gaps":["Systematic substrate catalogue for mammalian ZYG11B lacking","ZYG11B vs ZER1 functional redundancy and specificity unresolved","Regulation of ZYG11B expression, stability, and dimerization poorly understood"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,3,5,8,9,10]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4,11]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,5,8,9,10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[7,10]}],"complexes":["CRL2^ZYG11B (CUL2-EloB-EloC-ZYG11B)"],"partners":["CUL2","ELOB","ELOC","CGAS","NLRP1","VP1"],"other_free_text":[]},"mechanistic_narrative":"ZYG11B is the substrate-recognition subunit of the CRL2^ZYG11B E3 ubiquitin ligase, functioning as the principal N-recognin of the Gly/N-degron pathway to target proteins bearing unacetylated N-terminal glycine—and other small N-terminal residues (Ser, Ala, Cys)—for proteasomal degradation [PMID:34214466, PMID:36496439]. ZYG11B binds EloB/EloC adaptors through a VHL-box motif and engages substrates via its armadillo repeat domain, which forms a deep acidic pocket that hydrogen-bonds the free α-amino group of the N-terminal glycine; full-length ZYG11B adopts a seahorse-like architecture and can dimerize to present two substrate-binding sites, with all three interfaces—adaptor recruitment, substrate binding, and dimerization—required for degradation [PMID:17304241, PMID:34214466, PMID:41917018]. Physiological substrates include meiotic cyclin B in C. elegans, the NLRP1 inflammasome sensor after viral protease cleavage, and enterovirus EV71 VP1, while ZYG11B also enhances cGAS-DNA condensation to amplify innate immune signaling independently of its E3 ligase activity [PMID:15215208, PMID:40135890, PMID:36933219]. A truncating ZYG11B mutation disrupts protein localization, and zebrafish knockdown causes craniofacial cartilage and notochord defects linked to SOX6 dysregulation [PMID:32738032]."},"prefetch_data":{"uniprot":{"accession":"Q9C0D3","full_name":"Protein zyg-11 homolog B","aliases":[],"length_aa":744,"mass_kda":83.9,"function":"Serves as substrate adapter subunit in the E3 ubiquitin ligase complex ZYG11B-CUL2-Elongin BC. Acts to target substrates bearing N-terminal degrons for proteasomal degradation with the first four residues of substrates being the key recognition elements (PubMed:33093214, PubMed:34214466, PubMed:35636250). Prefers Nt-Gly but also has the capacity to recognize Nt-Ser, -Ala and -Cys (PubMed:36496439). Involved in the clearance of proteolytic fragments generated by caspase cleavage during apoptosis since N-terminal glycine degrons are strongly enriched at caspase cleavage sites. Also important in the quality control of protein N-myristoylation in which N-terminal glycine degrons are conditionally exposed after a failure of N-myristoylation (PubMed:31273098). In addition, plays a role in the amplification of cGAS to enhance innate immune response. Mechanistically, strengthens the processes of cGAS binding with dsDNA and assembling oligomers and also accelerates and stabilizes cGAS-DNA condensation, thereby enhancing production of antiviral IFNs and inflammatory cytokines (PubMed:36933219)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9C0D3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZYG11B","classification":"Not Classified","n_dependent_lines":27,"n_total_lines":1208,"dependency_fraction":0.022350993377483443},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZYG11B","total_profiled":1310},"omim":[{"mim_id":"618675","title":"ZYG11 FAMILY, MEMBER A, CELL CYCLE REGULATOR; ZYG11A","url":"https://www.omim.org/entry/618675"},{"mim_id":"618673","title":"ZYG11 FAMILY, MEMBER B, CELL CYCLE REGULATOR; ZYG11B","url":"https://www.omim.org/entry/618673"},{"mim_id":"617764","title":"ZYG11-RELATED CELL CYCLE REGULATOR; ZER1","url":"https://www.omim.org/entry/617764"},{"mim_id":"606636","title":"NLR FAMILY, PYRIN DOMAIN-CONTAINING 1; NLRP1","url":"https://www.omim.org/entry/606636"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":73.8},{"tissue":"tongue","ntpm":57.8}],"url":"https://www.proteinatlas.org/search/ZYG11B"},"hgnc":{"alias_symbol":["FLJ13456"],"prev_symbol":["ZYG11"]},"alphafold":{"accession":"Q9C0D3","domains":[{"cath_id":"-","chopping":"335-443","consensus_level":"medium","plddt":95.0582,"start":335,"end":443}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C0D3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C0D3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C0D3-F1-predicted_aligned_error_v6.png","plddt_mean":92.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZYG11B","jax_strain_url":"https://www.jax.org/strain/search?query=ZYG11B"},"sequence":{"accession":"Q9C0D3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C0D3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C0D3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C0D3"}},"corpus_meta":[{"pmid":"15215208","id":"PMC_15215208","title":"Zyg-11 and cul-2 regulate progression through meiosis II and polarity establishment in C. elegans.","date":"2004","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15215208","citation_count":108,"is_preprint":false},{"pmid":"15215209","id":"PMC_15215209","title":"CUL-2 and ZYG-11 promote meiotic anaphase II and the proper placement of the anterior-posterior axis in C. elegans.","date":"2004","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15215209","citation_count":77,"is_preprint":false},{"pmid":"17304241","id":"PMC_17304241","title":"The Caenorhabditis elegans cell-cycle regulator ZYG-11 defines a conserved family of CUL-2 complex components.","date":"2007","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/17304241","citation_count":47,"is_preprint":false},{"pmid":"34214466","id":"PMC_34214466","title":"Molecular basis for recognition of Gly/N-degrons by CRL2ZYG11B and CRL2ZER1.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/34214466","citation_count":35,"is_preprint":false},{"pmid":"33827988","id":"PMC_33827988","title":"ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/33827988","citation_count":31,"is_preprint":false},{"pmid":"2325632","id":"PMC_2325632","title":"Molecular analysis of zyg-11, a maternal-effect gene required for early embryogenesis of Caenorhabditis elegans.","date":"1990","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/2325632","citation_count":28,"is_preprint":false},{"pmid":"32738032","id":"PMC_32738032","title":"Functional and genetic analyses of ZYG11B provide evidences for its involvement in OAVS.","date":"2020","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32738032","citation_count":26,"is_preprint":false},{"pmid":"36496439","id":"PMC_36496439","title":"CRL2ZER1/ZYG11B recognizes small N-terminal residues for degradation.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36496439","citation_count":25,"is_preprint":false},{"pmid":"36933219","id":"PMC_36933219","title":"ZYG11B potentiates the antiviral innate immune response by enhancing cGAS-DNA binding and condensation.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36933219","citation_count":19,"is_preprint":false},{"pmid":"36847071","id":"PMC_36847071","title":"LncRNA LINC01871 sponging miR-142-3p to modulate ZYG11B promotes the chemoresistance of colorectal cancer cells by inducing autophagy.","date":"2023","source":"Anti-cancer drugs","url":"https://pubmed.ncbi.nlm.nih.gov/36847071","citation_count":14,"is_preprint":false},{"pmid":"11719588","id":"PMC_11719588","title":"Meiotic human sperm cells express a leucine-rich homologue of Caenorhabditis elegans early embryogenesis gene, Zyg-11.","date":"2001","source":"Molecular human reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/11719588","citation_count":10,"is_preprint":false},{"pmid":"40082426","id":"PMC_40082426","title":"Identification of a non-inhibitory aptameric ligand to CRL2ZYG11B E3 ligase for targeted protein degradation.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40082426","citation_count":8,"is_preprint":false},{"pmid":"35730627","id":"PMC_35730627","title":"Silencing of circular RNA‑ZYG11B exerts a neuroprotective effect against retinal neurodegeneration.","date":"2022","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35730627","citation_count":7,"is_preprint":false},{"pmid":"35636250","id":"PMC_35636250","title":"Structural insights into ORF10 recognition by ZYG11B.","date":"2022","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/35636250","citation_count":5,"is_preprint":false},{"pmid":"40135890","id":"PMC_40135890","title":"ZYG11B suppresses multiple enteroviruses by triggering viral VP1 degradation.","date":"2025","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/40135890","citation_count":3,"is_preprint":false},{"pmid":"41917018","id":"PMC_41917018","title":"Structures of ZYG11B-EloB-EloC-substrate complex reveal mechanisms of CRL2ZYG11B assembly and function.","date":"2026","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41917018","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.24.600508","title":"Structure of the E3 ligase CRL2-ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination","date":"2024-06-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.24.600508","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9084,"output_tokens":2982,"usd":0.035991},"stage2":{"model":"claude-opus-4-6","input_tokens":6337,"output_tokens":2835,"usd":0.15384},"total_usd":0.189831,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"C. elegans ZYG-11 acts as a component of a CUL-2-based E3 ubiquitin ligase that promotes the metaphase-to-anaphase transition at meiosis II by targeting cyclin B (CYB-3) for degradation; inactivation of ZYG-11 leads to CYB-3 accumulation and M phase arrest.\",\n      \"method\": \"RNAi knockdown in C. elegans, genetic epistasis, cyclin B accumulation assays\",\n      \"journal\": \"Development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated in two independent papers using RNAi and genetic analysis, consistent mechanistic conclusion across labs\",\n      \"pmids\": [\"15215208\", \"15215209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"ZYG-11 and CUL-2 regulate embryonic anterior-posterior polarity establishment in C. elegans, with their inactivation causing inverted PAR protein and P granule polarity; this polarity role can operate independently of their cell cycle progression function.\",\n      \"method\": \"RNAi knockdown, live imaging of PAR proteins and P granules in C. elegans embryos\",\n      \"journal\": \"Development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated in two independent papers with consistent epistasis and imaging data\",\n      \"pmids\": [\"15215208\", \"15215209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"ZYG-11 is the substrate-recognition subunit of a CUL-2-based ubiquitin ligase complex; it interacts with CUL-2 in vivo and binds the adaptor protein Elongin C via a nematode variant of the VHL-box motif, establishing ZYG11 family members as conserved CUL2 complex substrate receptors in nematodes and humans.\",\n      \"method\": \"Co-immunoprecipitation in vivo, VHL-box motif identification, sequence analysis of ZYG11 family across metazoa\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with functional domain identification, conserved across species\",\n      \"pmids\": [\"17304241\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZYG11B recognizes N-terminal glycine degrons (Gly/N-degrons) via its armadillo (ARM) repeat domain, which forms a deep, narrow cavity engaging the first four residues of the degron; the α-amino group of the glycine is accommodated by five conserved hydrogen bonds in an acidic pocket.\",\n      \"method\": \"Crystal structure of ZYG11B bound to Gly/N-degron peptides, biochemical binding assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures with biochemical validation, multiple Gly/N-degron substrates tested\",\n      \"pmids\": [\"34214466\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SARS-CoV-2 ORF10 interacts with ZYG11B (the substrate receptor of CRL2ZYG11B) through its N-terminus, which is critical for binding; however, ORF10 does not hijack or inhibit CRL2ZYG11B activity and ZYG11B/ZER1 are dispensable for SARS-CoV-2 infection in cultured cells.\",\n      \"method\": \"Co-immunoprecipitation, N-terminal deletion mapping, ZYG11B/ZER1 knockout cell infection assays, proteomics\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, deletion mapping, KO infection assays) in one study\",\n      \"pmids\": [\"33827988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ZYG11B (and ZER1) can recognize small N-terminal residues beyond glycine, including Nt-Ser, Nt-Ala, and Nt-Cys in vitro; Nt-acetylation of these residues by N-terminal acetyltransferases (NATs) shields them from ZYG11B recognition, revealing a role for CRL2ZYG11B in Nt-acetylation quality control.\",\n      \"method\": \"In vitro binding assays, crystal structures of ZYG11B bound to various small Nt-residue peptides, NAT-deficient cell degradation assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures combined with in vitro assays and cell-based functional validation\",\n      \"pmids\": [\"36496439\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Crystal structure of ZYG11B bound to the SARS-CoV-2 ORF10 N-terminal peptide reveals the molecular basis for ORF10 recognition by the ARM repeat domain of ZYG11B, consistent with Gly/N-degron recognition mechanism.\",\n      \"method\": \"Crystal structure determination of ZYG11B–ORF10 peptide complex\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with structural analysis of binding interface\",\n      \"pmids\": [\"35636250\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ZYG11B enhances cGAS-mediated innate immune responses by increasing cGAS-DNA binding affinity, potentiating cGAS-DNA condensation, and stabilizing the cGAS-DNA condensed complex; ZYG11B knockdown impairs cGAMP production and downstream interferon/cytokine transcription. Additionally, HSV-1 infection induces ZYG11B degradation to dampen this response.\",\n      \"method\": \"ZYG11B knockdown with cGAMP measurement, co-immunoprecipitation, DNA binding affinity assays, condensation assays, HSV-1 infection experiments\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple functional assays in single lab, mechanistic detail shown but not reconstituted in vitro\",\n      \"pmids\": [\"36933219\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZYG11B targets enterovirus EV71 structural protein VP1 for proteasomal degradation via the CRL2ZYG11B complex, driving K33-linked ubiquitination of VP1; the interaction between ZYG11B and VP1 was confirmed by mass spectrometry and immunoprecipitation, and key domains for VP1 and CUL2 binding were identified.\",\n      \"method\": \"Mass spectrometry, immunoprecipitation, ubiquitination assays, proteasome inhibition, domain mapping\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple methods (MS, Co-IP, ubiquitination assay) in single lab study\",\n      \"pmids\": [\"40135890\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cryo-EM structures of full-length human ZYG11B in complex with EloB-EloC adaptor and Gly/N-degron peptide reveal a seahorse-like architecture with distinct interfaces for adaptor binding and substrate engagement; ZYG11B can form both monomeric and dimeric assemblies, with the dimer stabilizing two substrate-binding sites in opposite orientations, and functional assays show all three interfaces (adaptor recruitment, substrate binding, dimerization) are essential for substrate degradation.\",\n      \"method\": \"Cryo-EM structure determination, functional ubiquitination/degradation assays with interface mutants\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structures of full-length complex combined with mutagenesis and functional degradation assays\",\n      \"pmids\": [\"41917018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structure of the CRL2-ZYG11B holoenzyme alone and in complex with NLRP1 Gly/N-degron peptide shows ZYG11B folds into an LRR domain followed by two ARM repeat domains that mediate CRL2 assembly and substrate recognition; ZYG11B promotes NLRP1 inflammasome activation by recognizing and ubiquitinating the NLRP1 Gly/N-degron revealed after viral protease cleavage.\",\n      \"method\": \"Cryo-EM structure determination, in vitro ubiquitination assays, NLRP1 inflammasome activation assays, blocking experiments\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structures with functional validation, but preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.06.24.600508\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A truncating mutation in human ZYG11B (p.Glu537*) alters subcellular localization of the truncated protein in HeLa cells; morpholino knockdown of zebrafish ZYG11B homologue disrupts craniofacial cartilage architecture and notochord development; ZYG11B expression regulates the cartilage master regulator SOX6 and is regulated by retinoic acid.\",\n      \"method\": \"Immunofluorescence of mutant ZYG11B in HeLa cells, morpholino knockdown in zebrafish, RT-PCR for SOX6 regulation\",\n      \"journal\": \"Molecular genetics & genomic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct localization experiment and in vivo knockdown with defined phenotype, single lab\",\n      \"pmids\": [\"32738032\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZYG11B is the substrate-recognition subunit of the CRL2ZYG11B E3 ubiquitin ligase complex, binding EloB/EloC adaptors via a VHL-box motif and engaging substrates through its armadillo (ARM) repeat domain, which forms a deep cavity that specifically recognizes N-terminal glycine (and other small unacetylated N-terminal residues) to drive Gly/N-degron pathway proteasomal degradation; structurally, full-length ZYG11B adopts a seahorse-like architecture that can dimerize to present two substrate-binding sites, and functionally ZYG11B targets cell cycle regulators (cyclin B), viral proteins (EV71 VP1 via K33-linked ubiquitination), and immune sensors (NLRP1 Gly/N-degron after viral protease cleavage), while also enhancing cGAS-DNA condensation to amplify innate immune responses.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ZYG11B is the substrate-recognition subunit of the CRL2^ZYG11B E3 ubiquitin ligase, functioning as the principal N-recognin of the Gly/N-degron pathway to target proteins bearing unacetylated N-terminal glycine—and other small N-terminal residues (Ser, Ala, Cys)—for proteasomal degradation [PMID:34214466, PMID:36496439]. ZYG11B binds EloB/EloC adaptors through a VHL-box motif and engages substrates via its armadillo repeat domain, which forms a deep acidic pocket that hydrogen-bonds the free α-amino group of the N-terminal glycine; full-length ZYG11B adopts a seahorse-like architecture and can dimerize to present two substrate-binding sites, with all three interfaces—adaptor recruitment, substrate binding, and dimerization—required for degradation [PMID:17304241, PMID:34214466, PMID:41917018]. Physiological substrates include meiotic cyclin B in C. elegans, the NLRP1 inflammasome sensor after viral protease cleavage, and enterovirus EV71 VP1, while ZYG11B also enhances cGAS-DNA condensation to amplify innate immune signaling independently of its E3 ligase activity [PMID:15215208, PMID:40135890, PMID:36933219]. A truncating ZYG11B mutation disrupts protein localization, and zebrafish knockdown causes craniofacial cartilage and notochord defects linked to SOX6 dysregulation [PMID:32738032].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing ZYG-11 as a CUL-2-linked cell-cycle regulator answered the question of how meiosis II metaphase-to-anaphase transition is controlled in C. elegans embryos, revealing cyclin B as a degradation target and an additional role in anterior-posterior polarity.\",\n      \"evidence\": \"RNAi knockdown and genetic epistasis in C. elegans embryos, live imaging of PAR proteins and P granules\",\n      \"pmids\": [\"15215208\", \"15215209\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct biochemical interaction between ZYG-11 and cyclin B not demonstrated\",\n        \"Whether polarity function requires ubiquitin ligase activity or acts through a separate mechanism\",\n        \"Mammalian homolog function unknown\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrating that ZYG-11 directly binds CUL-2 and Elongin C via a VHL-box motif established ZYG11 family proteins as bona fide CRL2 substrate-recognition subunits conserved from nematodes to humans.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation in vivo, VHL-box motif identification and cross-species sequence analysis\",\n      \"pmids\": [\"17304241\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No substrate identified for the mammalian ZYG11B paralog\",\n        \"Structural basis of adaptor and substrate engagement unknown\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A human truncating ZYG11B mutation and zebrafish knockdown linked ZYG11B to craniofacial cartilage and notochord development, revealing a vertebrate developmental function and SOX6 as a downstream regulated gene.\",\n      \"evidence\": \"Immunofluorescence of mutant protein in HeLa cells, morpholino knockdown in zebrafish, RT-PCR\",\n      \"pmids\": [\"32738032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether SOX6 regulation is direct (i.e., SOX6 is a ubiquitination substrate) or indirect\",\n        \"Single lab, no independent replication of zebrafish phenotype\",\n        \"Mechanism connecting ZYG11B E3 ligase activity to cartilage morphogenesis not defined\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Crystal structures of ZYG11B bound to Gly/N-degron peptides solved the long-standing question of how the CRL2^ZYG11B complex selects substrates, revealing a narrow ARM-repeat cavity that specifically accommodates the unmodified α-amino group of N-terminal glycine through five conserved hydrogen bonds.\",\n      \"evidence\": \"Crystal structure determination with multiple Gly/N-degron peptides, biochemical binding assays\",\n      \"pmids\": [\"34214466\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether additional sequence context beyond the first four residues influences substrate selectivity in vivo\",\n        \"Full-length ZYG11B architecture not yet resolved\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Testing the hypothesis that SARS-CoV-2 ORF10 hijacks CRL2^ZYG11B showed that while ORF10 binds ZYG11B via its N-terminus consistent with Gly/N-degron recognition, it neither co-opts nor inhibits the ligase, and ZYG11B is dispensable for infection.\",\n      \"evidence\": \"Co-immunoprecipitation, N-terminal deletion mapping, ZYG11B/ZER1 knockout cell infection assays, proteomics\",\n      \"pmids\": [\"33827988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether ORF10 binding has functional consequences in non-cultured-cell contexts\",\n        \"Whether ORF10 is degraded by CRL2^ZYG11B in vivo\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Expanding the substrate specificity of ZYG11B beyond glycine to include unacetylated Nt-Ser, Nt-Ala, and Nt-Cys established CRL2^ZYG11B as a quality-control mechanism that degrades proteins escaping N-terminal acetylation.\",\n      \"evidence\": \"Crystal structures of ZYG11B with various small-residue peptides, in vitro binding assays, NAT-deficient cell degradation assays\",\n      \"pmids\": [\"36496439\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Endogenous substrates accumulating in NAT-deficient cells due to ZYG11B have not been comprehensively catalogued\",\n        \"Relative contribution of ZYG11B versus ZER1 to Nt-acetylation quality control unclear\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating that ZYG11B enhances cGAS-DNA condensation and cGAMP production revealed an unexpected innate immunity function apparently independent of its canonical E3 ligase role, with HSV-1 degrading ZYG11B as a countermeasure.\",\n      \"evidence\": \"ZYG11B knockdown, cGAMP measurement, co-immunoprecipitation, DNA binding affinity and condensation assays, HSV-1 infection\",\n      \"pmids\": [\"36933219\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether ZYG11B's ubiquitin ligase activity contributes to cGAS regulation not resolved\",\n        \"Mechanism by which HSV-1 targets ZYG11B for degradation not identified\",\n        \"Not independently replicated\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of enterovirus VP1 as a ZYG11B substrate demonstrated that CRL2^ZYG11B serves as an antiviral E3 ligase mediating K33-linked ubiquitination and proteasomal degradation of a viral structural protein.\",\n      \"evidence\": \"Mass spectrometry, immunoprecipitation, ubiquitination assays with linkage typing, proteasome inhibition, domain mapping\",\n      \"pmids\": [\"40135890\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether VP1 targeting depends on a Gly/N-degron or an alternative recognition mode not clarified\",\n        \"In vivo antiviral significance not tested in animal models\",\n        \"Single lab study\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Cryo-EM structures of full-length human ZYG11B–EloBC with substrate peptide resolved the overall seahorse-like architecture and revealed functionally essential dimerization, showing that two substrate-binding sites in opposing orientations are required for efficient degradation.\",\n      \"evidence\": \"Cryo-EM of monomeric and dimeric assemblies, mutagenesis of adaptor, substrate, and dimer interfaces with degradation assays\",\n      \"pmids\": [\"41917018\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Physiological significance of dimer versus monomer in cells not established\",\n        \"No structure of a full substrate (rather than peptide) bound to the holoenzyme\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the comprehensive identification of endogenous Gly/N-degron substrates in mammalian cells, the functional division of labor between ZYG11B and its paralog ZER1, whether ZYG11B dimerization is regulated, and the molecular mechanism by which ZYG11B enhances cGAS condensation independently of ubiquitination.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Systematic substrate catalogue for mammalian ZYG11B lacking\",\n        \"ZYG11B vs ZER1 functional redundancy and specificity unresolved\",\n        \"Regulation of ZYG11B expression, stability, and dimerization poorly understood\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 3, 5, 8, 9, 10]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 5, 8, 9, 10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [7, 10]}\n    ],\n    \"complexes\": [\n      \"CRL2^ZYG11B (CUL2-EloB-EloC-ZYG11B)\"\n    ],\n    \"partners\": [\n      \"CUL2\",\n      \"ELOB\",\n      \"ELOC\",\n      \"CGAS\",\n      \"NLRP1\",\n      \"VP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}