{"gene":"EIF3J","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2007,"finding":"Human eIF3j binds directly to the aminoacyl (A) site and mRNA entry channel of the 40S ribosomal subunit (decoding center), interacts with eIF1A, reduces 40S affinity for mRNA, and this affinity is restored upon recruitment of initiator tRNA even while eIF3j remains in the mRNA-binding cleft, indicating eIF3j regulates access of the mRNA-binding cleft in response to initiation factor binding.","method":"Directed hydroxyl radical probing of human 40S ribosomal subunit complexes","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct structural probing method with multiple functional readouts (mRNA affinity, tRNA interplay, eIF1A interaction) in a focused mechanistic study","pmids":["17588516"],"is_preprint":false},{"year":2006,"finding":"The N-terminal 69-amino acid peptide of human eIF3j binds specifically to the rear alpha-helices of the eIF3b RNA recognition motif (RRM), and this interaction is essential for eIF3b-RRM recruitment to the 40S ribosomal subunit.","method":"NMR solution structure of eIF3b-RRM; binding assays identifying eIF3j N-terminal peptide as sufficient for eIF3b-RRM interaction and 40S recruitment","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure plus functional binding assay in a single focused study with multiple orthogonal methods","pmids":["17190833"],"is_preprint":false},{"year":2010,"finding":"A conserved tryptophan in the human eIF3j N-terminal acidic motif (NTA) is held in the helix α1/loop 5 hydrophobic pocket of the human eIF3b RRM. Mutating the corresponding yeast residues eliminates eIF3j/HCR1 association with eIF3b/PRT1 in vitro and in vivo, reduces 40S occupancy of eIF3, and produces a leaky scanning (AUG selection) defect partially suppressed by overexpressed eIF1A. eIF3j/HCR1 was found to interact with small ribosomal proteins RPS2 and RPS23 near the mRNA entry channel.","method":"NMR spectroscopy (solution structure of eIF3j NTA–eIF3b RRM interaction); yeast genetics (growth assays, leaky scanning reporter); co-immunoprecipitation; in vitro binding assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure plus mutagenesis plus in vivo genetic suppression, multiple orthogonal methods in one rigorous study","pmids":["20060839"],"is_preprint":false},{"year":2010,"finding":"The C-terminal domain (CTD) of yeast eIF3a/Tif32 interacts with eIF3j/HCR1 and eIF3b/Prt1, and the eIF3j/HCR1 CTD is required for its binding to eIF3a. The eIF3b-RRM–eIF3j/HCR1–eIF3a-CTD module functions near the mRNA entry channel to regulate the transition between scanning-conducive and initiation-competent conformations of the preinitiation complex (PIC), and the eIF3a CTD binds ribosomal proteins Rps2 and Rps3.","method":"Yeast genetic analysis (substitution mutants, growth phenotypes, leaky scanning assays); co-immunoprecipitation; in vitro binding assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus co-IP, single lab, multiple orthogonal methods","pmids":["20584985"],"is_preprint":false},{"year":2001,"finding":"Yeast eIF3j/Hcr1p is an RNA-binding protein that (1) binds to and stabilizes the multifactor complex (eIFs 1, 2, 3, 5 + Met-tRNA), (2) enhances a late cytoplasmic step in 40S ribosome maturation (20S pre-rRNA to 18S rRNA processing), and (3) its deletion causes decreased 40S subunits, paromomycin hypersensitivity, and synthetic lethality with drs2Δ or rps0aΔ. Human p35/eIF3j associates with yeast eIF3 and 43S initiation complexes in vitro and in vivo but does not complement the 40S biogenesis defect of hcr1Δ.","method":"Yeast genetics (deletion analysis, synthetic lethality, complementation); immunofluorescence localization; in vitro and in vivo co-immunoprecipitation; Northern blot (20S pre-rRNA accumulation)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal genetic and biochemical methods, replicated across yeast and human ortholog","pmids":["11560931"],"is_preprint":false},{"year":2015,"finding":"Cryo-EM structure of a yeast 40S–eIF1–eIF1A–eIF3–eIF3j initiation complex reveals that eIF3j makes direct contact with eIF1A and shows the network of interactions among eIF3 subunits, with differences in initiation-complex binding compared to mammalian eIF3.","method":"Cryo-electron microscopy with placement of prior X-ray/NMR structures","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with prior structural data integrated; direct eIF3j–eIF1A contact established structurally","pmids":["25664723"],"is_preprint":false},{"year":2015,"finding":"Protein kinase CK2 interacts with eIF3j and phosphorylates it at Ser127. Inhibition or knockdown of CK2 causes dissociation of eIF3j from the eIF3 complex. Expression of the Ser127Ala mutant impairs eIF3j association with other eIF3 subunits and reduces overall protein synthesis, demonstrating that CK2-mediated phosphorylation of eIF3j at Ser127 is required for eIF3 complex assembly and translation initiation.","method":"Co-immunoprecipitation; mass spectrometry; glycerol gradient sedimentation; CK2 inhibitor (CX-4945) and siRNA knockdown; Ser127Ala mutagenesis; protein synthesis assay","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro phosphorylation plus mutagenesis plus functional complex-assembly assay plus translation readout, multiple orthogonal methods in single study","pmids":["25887626"],"is_preprint":false},{"year":2019,"finding":"In yeast, loss of Hcr1/eIF3j leads to reinitiation of translation in 3′ UTRs consistent with a recycling defect; the defect is in 60S subunit recycling (not 40S), because reinitiation does not require an AUG codon and is suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Hcr1 overexpression cannot compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1, and loss of Hcr1 triggers increased RLI1 expression via an apparent feedback loop.","method":"Ribosome profiling (genome-wide); reporter translation assays; genetic overexpression/deletion epistasis in yeast","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — ribosome profiling plus genetic epistasis plus reporter assays, multiple orthogonal methods establishing 60S recycling role in vivo","pmids":["31269449"],"is_preprint":false},{"year":2021,"finding":"Human eIF3j stimulates peptidyl-tRNA hydrolysis induced by the eRF1–eRF3 release factor complex in a reconstituted mammalian in vitro translation system. eIF3j activity in termination is enhanced by co-presence of the eIF3 complex. eIF3j interacts with the pre-termination ribosomal complex, and eRF3 destabilizes this interaction. In solution, eIF3j binds eRF1, eRF3, and PABP in the presence of GTP. Toe-printing established that eIF3j acts at the step of release factor loading into the A-site, before GTP hydrolysis.","method":"Reconstituted mammalian in vitro translation system; peptide release assay; toe-printing assay; pull-down binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro translation system with multiple functional assays (hydrolysis, toe-printing, binding) in single focused study","pmids":["34591963"],"is_preprint":false},{"year":2022,"finding":"Drosophila eIF3j (the eIF3-associated factor) inhibits translation of the circular RNA circSfl. Mechanistically, eIF3j binding to circSfl promotes dissociation of the eIF3 complex from the circRNA. The C-terminus of eIF3j and an RNA regulon within the circSfl UTR are essential for this inhibitory effect. eIF3j-mediated circRNA translation repression is physiologically relevant during heat shock response.","method":"Drosophila eIF3j screen (all 43 eIFs tested); circRNA translation reporter assays; domain deletion/mutagenesis; in vivo heat shock experiments","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional screen plus domain mutagenesis plus in vivo validation in Drosophila, single lab","pmids":["36330957"],"is_preprint":false}],"current_model":"EIF3J encodes a peripherally/loosely associated subunit of the eIF3 complex that occupies the ribosomal decoding center (A-site and mRNA entry channel of the 40S subunit), where it interacts with eIF1A, reduces mRNA affinity, and cooperates with the eIF3b-RRM to regulate scanning and stringent AUG selection; it requires CK2-mediated phosphorylation at Ser127 for stable incorporation into the eIF3 complex; it promotes translation termination by facilitating loading of eRF1–eRF3 release factors into the ribosomal A-site; it assists 60S ribosomal subunit recycling after termination in vivo; it plays a dual role in 40S ribosome biogenesis (20S pre-rRNA processing) in yeast; and it can inhibit cap-independent translation of certain circular RNAs by displacing eIF3 from the circRNA."},"narrative":{"mechanistic_narrative":"EIF3J encodes a peripherally associated subunit of the eIF3 complex that occupies the decoding center of the small ribosomal subunit and acts as a regulatory hub across multiple steps of the translation cycle [PMID:17588516, PMID:25664723]. It binds directly within the aminoacyl (A) site and mRNA entry channel of the 40S subunit, where it contacts eIF1A and lowers the affinity of the 40S for mRNA; this affinity is restored upon initiator-tRNA recruitment, positioning eIF3j as a gatekeeper of the mRNA-binding cleft during initiation [PMID:17588516, PMID:25664723]. Its N-terminal acidic motif anchors a conserved tryptophan into a hydrophobic pocket of the eIF3b RNA-recognition motif, an interaction required to recruit the eIF3b-RRM to the 40S and to support stringent AUG selection during scanning; together with the eIF3a C-terminal domain near the mRNA entry channel, this module governs the transition between scanning-conducive and initiation-competent preinitiation-complex conformations [PMID:17190833, PMID:20060839, PMID:20584985]. Stable incorporation of eIF3j into eIF3 requires CK2-mediated phosphorylation at Ser127, and loss of this modification disrupts complex assembly and reduces global protein synthesis [PMID:25887626]. Beyond initiation, eIF3j promotes translation termination by facilitating loading of the eRF1–eRF3 release-factor complex into the A-site prior to GTP hydrolysis, and assists post-termination ribosome recycling, with the yeast ortholog Hcr1 specifically required for 60S subunit recycling [PMID:31269449, PMID:34591963]. The yeast protein additionally functions in late cytoplasmic 40S biogenesis, enhancing 20S pre-rRNA processing to 18S rRNA [PMID:11560931], and the Drosophila ortholog represses cap-independent translation of a circular RNA by displacing eIF3 from the transcript during the heat-shock response [PMID:36330957].","teleology":[{"year":2001,"claim":"Established eIF3j/Hcr1 as more than a passive eIF3 subunit by showing it binds RNA, stabilizes the multifactor initiation complex, and is required for late cytoplasmic 40S ribosome maturation, linking the protein to both initiation and subunit biogenesis.","evidence":"Yeast deletion/synthetic lethality genetics, immunofluorescence, co-IP, and Northern blots of 20S pre-rRNA in yeast with human ortholog tested for complementation","pmids":["11560931"],"confidence":"High","gaps":["Human p35/eIF3j failed to complement the yeast 40S biogenesis defect, leaving the conservation of the biogenesis role unresolved","Mechanism coupling multifactor-complex stabilization to pre-rRNA processing not defined"]},{"year":2006,"claim":"Mapped the physical basis of eIF3j–eIF3b coupling by showing the eIF3j N-terminal 69-residue peptide binds the eIF3b-RRM and is essential for recruiting the RRM to the 40S, defining how eIF3j anchors part of the eIF3 core to the ribosome.","evidence":"NMR solution structure of eIF3b-RRM plus peptide binding and 40S recruitment assays","pmids":["17190833"],"confidence":"High","gaps":["Functional consequence of the interaction for scanning or AUG selection not yet tested","Did not address eIF3j contacts with the ribosome itself"]},{"year":2007,"claim":"Located eIF3j at the ribosomal decoding center and revealed its gatekeeper logic, showing it occupies the A-site and mRNA entry channel, lowers 40S–mRNA affinity, contacts eIF1A, and responds to initiator-tRNA recruitment.","evidence":"Directed hydroxyl radical probing of human 40S complexes with multiple functional readouts","pmids":["17588516"],"confidence":"High","gaps":["Did not resolve how cleft access is communicated to downstream scanning","Static probing rather than dynamic measurement of the conformational transition"]},{"year":2010,"claim":"Connected the eIF3j–eIF3b–eIF3a module structurally and genetically to AUG selection fidelity, demonstrating that a conserved tryptophan anchors eIF3j to the eIF3b-RRM and that disrupting it causes leaky scanning suppressible by eIF1A overexpression.","evidence":"NMR structure of the NTA–RRM interface, yeast mutagenesis with leaky-scanning reporters, co-IP, and in vitro binding (two complementary studies)","pmids":["20060839","20584985"],"confidence":"Medium","gaps":["The eIF3a-CTD contributions rest on single-lab genetic epistasis plus co-IP","How the module toggles between scanning and initiation-competent conformations not directly visualized"]},{"year":2015,"claim":"Provided a structural snapshot of eIF3j in an assembled initiation complex and identified the regulatory switch controlling its incorporation, showing direct eIF3j–eIF1A contact by cryo-EM and that CK2 phosphorylation at Ser127 is required for eIF3 assembly and global translation.","evidence":"Cryo-EM of a yeast 40S–eIF1–eIF1A–eIF3–eIF3j complex; and CK2 inhibitor/knockdown, mass spectrometry, Ser127Ala mutagenesis, and protein-synthesis assays (two studies)","pmids":["25664723","25887626"],"confidence":"High","gaps":["Cryo-EM noted differences between yeast and mammalian eIF3 binding that were not fully reconciled","Upstream signals controlling CK2-dependent eIF3j phosphorylation unknown"]},{"year":2019,"claim":"Extended eIF3j function beyond initiation to ribosome recycling, showing in yeast that loss of Hcr1 causes AUG-independent 3'UTR reinitiation attributable to a 60S (not 40S) recycling defect, suppressed by Rli1/ABCE1 overexpression.","evidence":"Genome-wide ribosome profiling, reporter assays, and overexpression/deletion epistasis in yeast","pmids":["31269449"],"confidence":"High","gaps":["Molecular mechanism by which eIF3j assists 60S recycling not defined","Conservation of the recycling role in mammals not tested here"]},{"year":2021,"claim":"Defined a direct role for human eIF3j in translation termination, showing it stimulates eRF1–eRF3-induced peptidyl-tRNA hydrolysis by acting at the release-factor loading step prior to GTP hydrolysis.","evidence":"Reconstituted mammalian in vitro translation, peptide-release and toe-printing assays, and pull-downs with eRF1, eRF3, and PABP","pmids":["34591963"],"confidence":"High","gaps":["Structural basis of eIF3j positioning during termination not resolved","Relationship between the termination role and the 60S recycling role not integrated"]},{"year":2022,"claim":"Revealed a repressive role for eIF3j in cap-independent circular RNA translation, showing that in Drosophila it displaces eIF3 from circSfl via its C-terminus and a UTR RNA regulon, with physiological relevance during heat shock.","evidence":"Drosophila eIF screen, circRNA translation reporters, domain mutagenesis, and in vivo heat-shock experiments","pmids":["36330957"],"confidence":"Medium","gaps":["Single-lab study in Drosophila; conservation of circRNA repression in mammals untested","How eIF3j discriminates circRNA from canonical mRNA substrates unclear"]},{"year":null,"claim":"How eIF3j's distinct roles across initiation gatekeeping, AUG fidelity, termination, ribosome recycling, and circRNA repression are coordinated within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified structural model spanning initiation, termination, and recycling states","Regulatory inputs (beyond CK2) that partition eIF3j among these functions unknown","Mammalian relevance of the yeast biogenesis and recycling roles not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,8]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[0,7,8,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,5]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[4,7,9]}],"complexes":["eIF3","multifactor complex (eIF1/eIF2/eIF3/eIF5/Met-tRNA)","43S preinitiation complex"],"partners":["EIF3B","EIF3A","EIF1AX","ERF1","ERF3","PABPC1","RPS2","RPS23"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75822","full_name":"Eukaryotic translation initiation factor 3 subunit J","aliases":["Eukaryotic translation initiation factor 3 subunit 1","eIF-3-alpha","eIF3 p35"],"length_aa":258,"mass_kda":29.1,"function":"Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O75822/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/EIF3J","classification":"Common Essential","n_dependent_lines":924,"n_total_lines":1208,"dependency_fraction":0.7649006622516556},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ABCE1","stoichiometry":10.0},{"gene":"EIF3B","stoichiometry":10.0},{"gene":"EIF3G","stoichiometry":10.0},{"gene":"RPS16","stoichiometry":4.0},{"gene":"ATG4B","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DRG1","stoichiometry":0.2},{"gene":"EIF3K","stoichiometry":0.2},{"gene":"EIF5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/EIF3J","total_profiled":1310},"omim":[{"mim_id":"609596","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 3, SUBUNIT K; EIF3K","url":"https://www.omim.org/entry/609596"},{"mim_id":"609532","title":"HEPATITIS C VIRUS, SUSCEPTIBILITY TO","url":"https://www.omim.org/entry/609532"},{"mim_id":"603910","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 3, SUBUNIT J; EIF3J","url":"https://www.omim.org/entry/603910"},{"mim_id":"300160","title":"DEAD-BOX HELICASE 3, X-LINKED; DDX3X","url":"https://www.omim.org/entry/300160"},{"mim_id":"176981","title":"RECEPTOR FOR ACTIVATED PROTEIN KINASE C, 1; RACK1","url":"https://www.omim.org/entry/176981"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":196.4}],"url":"https://www.proteinatlas.org/search/EIF3J"},"hgnc":{"alias_symbol":["eIF3-p35","eIF3-alpha"],"prev_symbol":["EIF3S1"]},"alphafold":{"accession":"O75822","domains":[{"cath_id":"1.10.246.60","chopping":"149-218","consensus_level":"medium","plddt":94.9564,"start":149,"end":218},{"cath_id":"1.20.5","chopping":"77-106","consensus_level":"medium","plddt":72.6537,"start":77,"end":106},{"cath_id":"1.20.5","chopping":"108-137","consensus_level":"medium","plddt":85.9917,"start":108,"end":137}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75822","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75822-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75822-F1-predicted_aligned_error_v6.png","plddt_mean":68.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EIF3J","jax_strain_url":"https://www.jax.org/strain/search?query=EIF3J"},"sequence":{"accession":"O75822","fasta_url":"https://rest.uniprot.org/uniprotkb/O75822.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75822/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75822"}},"corpus_meta":[{"pmid":"33764843","id":"PMC_33764843","title":"Long noncoding RNA (lncRNA) EIF3J-DT induces chemoresistance of gastric cancer via autophagy activation.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/33764843","citation_count":197,"is_preprint":false},{"pmid":"17588516","id":"PMC_17588516","title":"eIF3j is located in the decoding center of the human 40S ribosomal subunit.","date":"2007","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/17588516","citation_count":108,"is_preprint":false},{"pmid":"25664723","id":"PMC_25664723","title":"Structure of a yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex.","date":"2015","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25664723","citation_count":84,"is_preprint":false},{"pmid":"20584985","id":"PMC_20584985","title":"The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons.","date":"2010","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20584985","citation_count":79,"is_preprint":false},{"pmid":"20060839","id":"PMC_20060839","title":"The indispensable N-terminal half of eIF3j/HCR1 cooperates with its structurally conserved binding partner eIF3b/PRT1-RRM and with eIF1A in stringent AUG selection.","date":"2010","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20060839","citation_count":76,"is_preprint":false},{"pmid":"11560931","id":"PMC_11560931","title":"Dual function of eIF3j/Hcr1p in processing 20 S pre-rRNA and translation initiation.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11560931","citation_count":56,"is_preprint":false},{"pmid":"17190833","id":"PMC_17190833","title":"Structure of eIF3b RNA recognition motif and its interaction with eIF3j: structural insights into the recruitment of eIF3b to the 40 S ribosomal 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biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31709617","citation_count":35,"is_preprint":false},{"pmid":"36330957","id":"PMC_36330957","title":"eIF3j inhibits translation of a subset of circular RNAs in eukaryotic cells.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/36330957","citation_count":31,"is_preprint":false},{"pmid":"32811869","id":"PMC_32811869","title":"LncRNA EIF3J-AS1 enhanced esophageal cancer invasion via regulating AKT1 expression through sponging miR-373-3p.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/32811869","citation_count":20,"is_preprint":false},{"pmid":"34591963","id":"PMC_34591963","title":"eIF3j facilitates loading of release factors into the ribosome.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34591963","citation_count":17,"is_preprint":false},{"pmid":"25887626","id":"PMC_25887626","title":"Protein kinase CK2 potentiates 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oryzae.","date":"2026","source":"Mycologia","url":"https://pubmed.ncbi.nlm.nih.gov/42118908","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11409,"output_tokens":3073,"usd":0.040161,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10404,"output_tokens":3569,"usd":0.070623,"stage2_stop_reason":"end_turn"},"total_usd":0.110784,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Human eIF3j binds directly to the aminoacyl (A) site and mRNA entry channel of the 40S ribosomal subunit (decoding center), interacts with eIF1A, reduces 40S affinity for mRNA, and this affinity is restored upon recruitment of initiator tRNA even while eIF3j remains in the mRNA-binding cleft, indicating eIF3j regulates access of the mRNA-binding cleft in response to initiation factor binding.\",\n      \"method\": \"Directed hydroxyl radical probing of human 40S ribosomal subunit complexes\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct structural probing method with multiple functional readouts (mRNA affinity, tRNA interplay, eIF1A interaction) in a focused mechanistic study\",\n      \"pmids\": [\"17588516\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The N-terminal 69-amino acid peptide of human eIF3j binds specifically to the rear alpha-helices of the eIF3b RNA recognition motif (RRM), and this interaction is essential for eIF3b-RRM recruitment to the 40S ribosomal subunit.\",\n      \"method\": \"NMR solution structure of eIF3b-RRM; binding assays identifying eIF3j N-terminal peptide as sufficient for eIF3b-RRM interaction and 40S recruitment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure plus functional binding assay in a single focused study with multiple orthogonal methods\",\n      \"pmids\": [\"17190833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A conserved tryptophan in the human eIF3j N-terminal acidic motif (NTA) is held in the helix α1/loop 5 hydrophobic pocket of the human eIF3b RRM. Mutating the corresponding yeast residues eliminates eIF3j/HCR1 association with eIF3b/PRT1 in vitro and in vivo, reduces 40S occupancy of eIF3, and produces a leaky scanning (AUG selection) defect partially suppressed by overexpressed eIF1A. eIF3j/HCR1 was found to interact with small ribosomal proteins RPS2 and RPS23 near the mRNA entry channel.\",\n      \"method\": \"NMR spectroscopy (solution structure of eIF3j NTA–eIF3b RRM interaction); yeast genetics (growth assays, leaky scanning reporter); co-immunoprecipitation; in vitro binding assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure plus mutagenesis plus in vivo genetic suppression, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"20060839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The C-terminal domain (CTD) of yeast eIF3a/Tif32 interacts with eIF3j/HCR1 and eIF3b/Prt1, and the eIF3j/HCR1 CTD is required for its binding to eIF3a. The eIF3b-RRM–eIF3j/HCR1–eIF3a-CTD module functions near the mRNA entry channel to regulate the transition between scanning-conducive and initiation-competent conformations of the preinitiation complex (PIC), and the eIF3a CTD binds ribosomal proteins Rps2 and Rps3.\",\n      \"method\": \"Yeast genetic analysis (substitution mutants, growth phenotypes, leaky scanning assays); co-immunoprecipitation; in vitro binding assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus co-IP, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"20584985\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Yeast eIF3j/Hcr1p is an RNA-binding protein that (1) binds to and stabilizes the multifactor complex (eIFs 1, 2, 3, 5 + Met-tRNA), (2) enhances a late cytoplasmic step in 40S ribosome maturation (20S pre-rRNA to 18S rRNA processing), and (3) its deletion causes decreased 40S subunits, paromomycin hypersensitivity, and synthetic lethality with drs2Δ or rps0aΔ. Human p35/eIF3j associates with yeast eIF3 and 43S initiation complexes in vitro and in vivo but does not complement the 40S biogenesis defect of hcr1Δ.\",\n      \"method\": \"Yeast genetics (deletion analysis, synthetic lethality, complementation); immunofluorescence localization; in vitro and in vivo co-immunoprecipitation; Northern blot (20S pre-rRNA accumulation)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal genetic and biochemical methods, replicated across yeast and human ortholog\",\n      \"pmids\": [\"11560931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cryo-EM structure of a yeast 40S–eIF1–eIF1A–eIF3–eIF3j initiation complex reveals that eIF3j makes direct contact with eIF1A and shows the network of interactions among eIF3 subunits, with differences in initiation-complex binding compared to mammalian eIF3.\",\n      \"method\": \"Cryo-electron microscopy with placement of prior X-ray/NMR structures\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with prior structural data integrated; direct eIF3j–eIF1A contact established structurally\",\n      \"pmids\": [\"25664723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Protein kinase CK2 interacts with eIF3j and phosphorylates it at Ser127. Inhibition or knockdown of CK2 causes dissociation of eIF3j from the eIF3 complex. Expression of the Ser127Ala mutant impairs eIF3j association with other eIF3 subunits and reduces overall protein synthesis, demonstrating that CK2-mediated phosphorylation of eIF3j at Ser127 is required for eIF3 complex assembly and translation initiation.\",\n      \"method\": \"Co-immunoprecipitation; mass spectrometry; glycerol gradient sedimentation; CK2 inhibitor (CX-4945) and siRNA knockdown; Ser127Ala mutagenesis; protein synthesis assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro phosphorylation plus mutagenesis plus functional complex-assembly assay plus translation readout, multiple orthogonal methods in single study\",\n      \"pmids\": [\"25887626\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In yeast, loss of Hcr1/eIF3j leads to reinitiation of translation in 3′ UTRs consistent with a recycling defect; the defect is in 60S subunit recycling (not 40S), because reinitiation does not require an AUG codon and is suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Hcr1 overexpression cannot compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1, and loss of Hcr1 triggers increased RLI1 expression via an apparent feedback loop.\",\n      \"method\": \"Ribosome profiling (genome-wide); reporter translation assays; genetic overexpression/deletion epistasis in yeast\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ribosome profiling plus genetic epistasis plus reporter assays, multiple orthogonal methods establishing 60S recycling role in vivo\",\n      \"pmids\": [\"31269449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Human eIF3j stimulates peptidyl-tRNA hydrolysis induced by the eRF1–eRF3 release factor complex in a reconstituted mammalian in vitro translation system. eIF3j activity in termination is enhanced by co-presence of the eIF3 complex. eIF3j interacts with the pre-termination ribosomal complex, and eRF3 destabilizes this interaction. In solution, eIF3j binds eRF1, eRF3, and PABP in the presence of GTP. Toe-printing established that eIF3j acts at the step of release factor loading into the A-site, before GTP hydrolysis.\",\n      \"method\": \"Reconstituted mammalian in vitro translation system; peptide release assay; toe-printing assay; pull-down binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro translation system with multiple functional assays (hydrolysis, toe-printing, binding) in single focused study\",\n      \"pmids\": [\"34591963\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Drosophila eIF3j (the eIF3-associated factor) inhibits translation of the circular RNA circSfl. Mechanistically, eIF3j binding to circSfl promotes dissociation of the eIF3 complex from the circRNA. The C-terminus of eIF3j and an RNA regulon within the circSfl UTR are essential for this inhibitory effect. eIF3j-mediated circRNA translation repression is physiologically relevant during heat shock response.\",\n      \"method\": \"Drosophila eIF3j screen (all 43 eIFs tested); circRNA translation reporter assays; domain deletion/mutagenesis; in vivo heat shock experiments\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional screen plus domain mutagenesis plus in vivo validation in Drosophila, single lab\",\n      \"pmids\": [\"36330957\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EIF3J encodes a peripherally/loosely associated subunit of the eIF3 complex that occupies the ribosomal decoding center (A-site and mRNA entry channel of the 40S subunit), where it interacts with eIF1A, reduces mRNA affinity, and cooperates with the eIF3b-RRM to regulate scanning and stringent AUG selection; it requires CK2-mediated phosphorylation at Ser127 for stable incorporation into the eIF3 complex; it promotes translation termination by facilitating loading of eRF1–eRF3 release factors into the ribosomal A-site; it assists 60S ribosomal subunit recycling after termination in vivo; it plays a dual role in 40S ribosome biogenesis (20S pre-rRNA processing) in yeast; and it can inhibit cap-independent translation of certain circular RNAs by displacing eIF3 from the circRNA.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EIF3J encodes a peripherally associated subunit of the eIF3 complex that occupies the decoding center of the small ribosomal subunit and acts as a regulatory hub across multiple steps of the translation cycle [#0, #5]. It binds directly within the aminoacyl (A) site and mRNA entry channel of the 40S subunit, where it contacts eIF1A and lowers the affinity of the 40S for mRNA; this affinity is restored upon initiator-tRNA recruitment, positioning eIF3j as a gatekeeper of the mRNA-binding cleft during initiation [#0, #5]. Its N-terminal acidic motif anchors a conserved tryptophan into a hydrophobic pocket of the eIF3b RNA-recognition motif, an interaction required to recruit the eIF3b-RRM to the 40S and to support stringent AUG selection during scanning; together with the eIF3a C-terminal domain near the mRNA entry channel, this module governs the transition between scanning-conducive and initiation-competent preinitiation-complex conformations [#1, #2, #3]. Stable incorporation of eIF3j into eIF3 requires CK2-mediated phosphorylation at Ser127, and loss of this modification disrupts complex assembly and reduces global protein synthesis [#6]. Beyond initiation, eIF3j promotes translation termination by facilitating loading of the eRF1–eRF3 release-factor complex into the A-site prior to GTP hydrolysis, and assists post-termination ribosome recycling, with the yeast ortholog Hcr1 specifically required for 60S subunit recycling [#7, #8]. The yeast protein additionally functions in late cytoplasmic 40S biogenesis, enhancing 20S pre-rRNA processing to 18S rRNA [#4], and the Drosophila ortholog represses cap-independent translation of a circular RNA by displacing eIF3 from the transcript during the heat-shock response [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established eIF3j/Hcr1 as more than a passive eIF3 subunit by showing it binds RNA, stabilizes the multifactor initiation complex, and is required for late cytoplasmic 40S ribosome maturation, linking the protein to both initiation and subunit biogenesis.\",\n      \"evidence\": \"Yeast deletion/synthetic lethality genetics, immunofluorescence, co-IP, and Northern blots of 20S pre-rRNA in yeast with human ortholog tested for complementation\",\n      \"pmids\": [\"11560931\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human p35/eIF3j failed to complement the yeast 40S biogenesis defect, leaving the conservation of the biogenesis role unresolved\", \"Mechanism coupling multifactor-complex stabilization to pre-rRNA processing not defined\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Mapped the physical basis of eIF3j–eIF3b coupling by showing the eIF3j N-terminal 69-residue peptide binds the eIF3b-RRM and is essential for recruiting the RRM to the 40S, defining how eIF3j anchors part of the eIF3 core to the ribosome.\",\n      \"evidence\": \"NMR solution structure of eIF3b-RRM plus peptide binding and 40S recruitment assays\",\n      \"pmids\": [\"17190833\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of the interaction for scanning or AUG selection not yet tested\", \"Did not address eIF3j contacts with the ribosome itself\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Located eIF3j at the ribosomal decoding center and revealed its gatekeeper logic, showing it occupies the A-site and mRNA entry channel, lowers 40S–mRNA affinity, contacts eIF1A, and responds to initiator-tRNA recruitment.\",\n      \"evidence\": \"Directed hydroxyl radical probing of human 40S complexes with multiple functional readouts\",\n      \"pmids\": [\"17588516\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how cleft access is communicated to downstream scanning\", \"Static probing rather than dynamic measurement of the conformational transition\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Connected the eIF3j–eIF3b–eIF3a module structurally and genetically to AUG selection fidelity, demonstrating that a conserved tryptophan anchors eIF3j to the eIF3b-RRM and that disrupting it causes leaky scanning suppressible by eIF1A overexpression.\",\n      \"evidence\": \"NMR structure of the NTA–RRM interface, yeast mutagenesis with leaky-scanning reporters, co-IP, and in vitro binding (two complementary studies)\",\n      \"pmids\": [\"20060839\", \"20584985\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The eIF3a-CTD contributions rest on single-lab genetic epistasis plus co-IP\", \"How the module toggles between scanning and initiation-competent conformations not directly visualized\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided a structural snapshot of eIF3j in an assembled initiation complex and identified the regulatory switch controlling its incorporation, showing direct eIF3j–eIF1A contact by cryo-EM and that CK2 phosphorylation at Ser127 is required for eIF3 assembly and global translation.\",\n      \"evidence\": \"Cryo-EM of a yeast 40S–eIF1–eIF1A–eIF3–eIF3j complex; and CK2 inhibitor/knockdown, mass spectrometry, Ser127Ala mutagenesis, and protein-synthesis assays (two studies)\",\n      \"pmids\": [\"25664723\", \"25887626\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cryo-EM noted differences between yeast and mammalian eIF3 binding that were not fully reconciled\", \"Upstream signals controlling CK2-dependent eIF3j phosphorylation unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended eIF3j function beyond initiation to ribosome recycling, showing in yeast that loss of Hcr1 causes AUG-independent 3'UTR reinitiation attributable to a 60S (not 40S) recycling defect, suppressed by Rli1/ABCE1 overexpression.\",\n      \"evidence\": \"Genome-wide ribosome profiling, reporter assays, and overexpression/deletion epistasis in yeast\",\n      \"pmids\": [\"31269449\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which eIF3j assists 60S recycling not defined\", \"Conservation of the recycling role in mammals not tested here\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined a direct role for human eIF3j in translation termination, showing it stimulates eRF1–eRF3-induced peptidyl-tRNA hydrolysis by acting at the release-factor loading step prior to GTP hydrolysis.\",\n      \"evidence\": \"Reconstituted mammalian in vitro translation, peptide-release and toe-printing assays, and pull-downs with eRF1, eRF3, and PABP\",\n      \"pmids\": [\"34591963\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of eIF3j positioning during termination not resolved\", \"Relationship between the termination role and the 60S recycling role not integrated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a repressive role for eIF3j in cap-independent circular RNA translation, showing that in Drosophila it displaces eIF3 from circSfl via its C-terminus and a UTR RNA regulon, with physiological relevance during heat shock.\",\n      \"evidence\": \"Drosophila eIF screen, circRNA translation reporters, domain mutagenesis, and in vivo heat-shock experiments\",\n      \"pmids\": [\"36330957\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study in Drosophila; conservation of circRNA repression in mammals untested\", \"How eIF3j discriminates circRNA from canonical mRNA substrates unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How eIF3j's distinct roles across initiation gatekeeping, AUG fidelity, termination, ribosome recycling, and circRNA repression are coordinated within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified structural model spanning initiation, termination, and recycling states\", \"Regulatory inputs (beyond CK2) that partition eIF3j among these functions unknown\", \"Mammalian relevance of the yeast biogenesis and recycling roles not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 8]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0, 7, 8, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [0, 5, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [4, 7, 9]}\n    ],\n    \"complexes\": [\"eIF3\", \"multifactor complex (eIF1/eIF2/eIF3/eIF5/Met-tRNA)\", \"43S preinitiation complex\"],\n    \"partners\": [\"EIF3B\", \"EIF3A\", \"EIF1AX\", \"ERF1\", \"ERF3\", \"PABPC1\", \"RPS2\", \"RPS23\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}