{"gene":"EIF3B","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":1994,"finding":"Purified yeast eIF3 is a ~550 kDa complex of eight subunits; the 90-kDa subunit corresponds to PRT1 (EIF3B ortholog). The complex promotes dissociation of 80S ribosomes into subunits, stabilizes Met-tRNAi binding to 40S ribosomal subunits, and is required for mRNA binding. The 62-kDa subunit (not PRT1/EIF3B itself) was identified as the RNA-binding subunit within the complex.","method":"Biochemical purification from ribosomal salt wash, molecular sieve and ion exchange chromatography, methionyl-puromycin synthesis assay, immunoblotting","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted activity in vitro, multiple orthogonal biochemical methods, foundational purification paper","pmids":["7798228"],"is_preprint":false},{"year":1995,"finding":"Prt1 (EIF3B ortholog) co-purifies with four other polypeptides (130, 80, 75, 40, 32 kDa) as a protein complex that restores translation in a cell-free system derived from temperature-sensitive prt1 mutant yeast, demonstrating the complex is an active translation factor. An N-terminal in-frame deletion generates a dominant-negative form that competes with wild-type Prt1 for incorporation into the complex and inhibits 40S ribosome binding.","method":"Multi-step protein purification, cell-free translation complementation assay, subcellular fractionation, dominant-negative deletion analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of translation activity, dominant-negative mutant analysis, multiple orthogonal methods","pmids":["7876188","7623843"],"is_preprint":false},{"year":1995,"finding":"Mutational analysis of yeast Prt1 (EIF3B ortholog) identified six independent temperature-sensitive missense mutations distributed throughout the central and C-terminal regions. An N-terminal in-frame deletion creates a dominant-negative form that inhibits 40S ribosome association of wild-type Prt1, indicating the N-terminal region is required for proper complex assembly.","method":"Temperature-sensitive mutant characterization, subcellular fractionation, dominant-negative mutant analysis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical analysis in yeast, single lab, multiple alleles tested","pmids":["7623843"],"is_preprint":false},{"year":1997,"finding":"Human PRT1 (EIF3B) is an integral subunit of human eIF3, migrating at 116 kDa. Far Western analysis shows that hPrt1 directly interacts with the p170 (eIF3a) subunit of eIF3. Mapping studies identify the RNA recognition motif (RRM) domain of hPrt1 as the region required for association with p170/eIF3a.","method":"cDNA cloning, immunoblotting with anti-eIF3 antibody, far Western analysis, domain deletion mapping","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — far Western (direct binding assay) with domain mapping; single lab","pmids":["8995410"],"is_preprint":false},{"year":1997,"finding":"The p110 subunit of mammalian eIF3, purified from rabbit reticulocyte lysates, was identified as the mammalian homologue of yeast Prt1p (EIF3B). The purified eIF3 complex (lacking p170) stimulated Met-tRNAf binding to 40S subunits, formed a functional 40S initiation complex at AUG, and was released from the 40S subunit during eIF5-dependent 60S subunit joining.","method":"Biochemical purification, cell-free initiation complex assembly assay, cDNA cloning and sequencing, immunochemical characterization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted initiation activity in vitro, multiple orthogonal methods, independent lab confirmation of Prt1 as core eIF3 subunit","pmids":["9388245"],"is_preprint":false},{"year":2001,"finding":"The RRM domain of yeast eIF3b/PRT1 interacts simultaneously with HCR1 (eIF3j ortholog) and with an internal domain of TIF32 (eIF3a ortholog). Removal of the PRT1 RRM in vivo caused dissociation of TIF32, NIP1, HCR1, and eIF5 from eIF3, and destroyed 40S ribosome binding by the residual PRT1-TIF34-TIF35 subcomplex. Genetic suppressor analysis linked PRT1, HCR1, and TIF32 functionally.","method":"In vivo co-immunoprecipitation, genetic suppressor analysis, deletion mutant analysis, ribosome binding assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, genetic epistasis, multiple deletion constructs, replicated across multiple subunit interactions","pmids":["11179233"],"is_preprint":false},{"year":2001,"finding":"Yeast Pci8p and human eIF3e/Int-6 both interact with the eIF3b/Prt1 subunit by binding to a discrete segment of Prt1p in vivo and in vitro. Human eIF3e/Int-6 interacts with the homologous segment of human eIF3b. This defines a specific interaction domain on eIF3b distinct from its RRM.","method":"In vivo and in vitro binding assays, domain mapping, two-hybrid analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo binding with domain mapping, single lab","pmids":["11457827"],"is_preprint":false},{"year":2006,"finding":"The solution structure of the N-terminal RRM domain of human eIF3b was determined by NMR. The RRM has a non-canonical fold with a negatively charged beta-sheet surface incompatible with RNA binding. Instead, eIF3j binds to the rear alpha-helices of eIF3b-RRM (opposite the beta-sheet). The N-terminal 69-amino acid peptide of eIF3j is sufficient for binding eIF3b-RRM, and this interaction is essential for eIF3b-RRM recruitment to the 40S ribosomal subunit.","method":"NMR structure determination, in vitro binding assays, 40S ribosome binding experiments","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with functional validation of binding interface, ribosome recruitment assay","pmids":["17190833"],"is_preprint":false},{"year":2006,"finding":"Mutating the RNP1 motif of yeast eIF3b/PRT1 (prt1-rnp1) impairs direct in vitro interactions with both eIF3a/TIF32 and eIF3j/HCR1, reduces 40S binding of eIF3 to native preinitiation complexes in vivo, reduces 40S-bound eIF5 and eIF1, and increases leaky scanning at GCN4 uORF1, indicating the PRT1 RNP1 motif is required for optimal preinitiation complex assembly and AUG recognition.","method":"Site-directed mutagenesis, in vitro pull-down, native preinitiation complex isolation, polysome/ribosome analysis, genetic reporter assay for leaky scanning","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — mutagenesis combined with in vitro binding, ribosome association, and genetic readouts; multiple orthogonal methods","pmids":["16581774"],"is_preprint":false},{"year":2010,"finding":"The eIF3b/PRT1 RRM and eIF3j/HCR1 N-terminal domain (NTD) both interact with the CTD of eIF3a/TIF32. Mutations in eIF3a and eIF3j that disrupt their interactions with the eIF3b RRM increase leaky scanning at an AUG codon. The extreme CTD of eIF3a/TIF32 binds ribosomal proteins Rps2 and Rps3, placing the eIF3b-RRM-eIF3j-eIF3a-CTD module near the mRNA entry channel.","method":"Genetic epistasis, in vitro pull-down, mutant phenotype analysis, ribosomal protein binding assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis and pull-down assays, single lab, multiple interacting subunits tested","pmids":["20584985"],"is_preprint":false},{"year":2010,"finding":"NMR structure of the human eIF3b-RRM/eIF3j NTA interaction: a conserved tryptophan in the eIF3j N-terminal acidic motif (NTA) is held in the helix alpha1/loop 5 hydrophobic pocket of eIF3b-RRM. Mutating corresponding 'pocket' residues in yeast eIF3b/PRT1 eliminates eIF3j/HCR1 association in vitro and in vivo, reduces 40S occupancy of eIF3, and produces leaky scanning defects suppressible by overexpressed eIF1A, indicating eIF3j remains on scanning preinitiation complexes and cooperates with eIF3b-RRM for AUG selection.","method":"NMR structure determination, in vitro and in vivo binding assays, 40S ribosome co-sedimentation, genetic suppressor analysis (eIF1A overexpression), translation reporter assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with mutagenesis validated in vivo and in vitro across multiple orthogonal assays","pmids":["20060839"],"is_preprint":false},{"year":2010,"finding":"Crystal structure of yeast eIF3b-RRM shows the same fold as human eIF3b-RRM with similar surface charge at the eIF3j-binding interface. Thermodynamic analysis confirms the same range of enthalpy change and dissociation constant for yeast and human eIF3b-RRM/eIF3j interactions. Unlike human eIF3b-RRM, the yeast RRM beta-sheet surface is compatible with RNA binding, and the yeast domain was confirmed to interact with yeast total RNA.","method":"X-ray crystallography, ITC thermodynamic analysis, RNA binding assay with yeast total RNA","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with ITC functional validation, single lab but multiple orthogonal methods","pmids":["20862284"],"is_preprint":false},{"year":2014,"finding":"Crystal structure of the WD40 domain of Chaetomium thermophilum eIF3b reveals a nine-bladed beta-propeller fold, conserved across all eIF3b orthologs. In vitro binding assays demonstrate that eIF3b directly binds 40S ribosomes and isolated ribosomal protein rpS9e, consistent with placement of eIF3b near the 40S subunit as suggested by cryo-EM reinterpretation.","method":"X-ray crystallography, cryo-EM map analysis, in vitro ribosome binding assay, direct binding to isolated rpS9e","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus direct in vitro binding to ribosome and ribosomal protein, orthogonal structural and biochemical methods","pmids":["24768115"],"is_preprint":false},{"year":2014,"finding":"P311 (an intrinsically disordered RNA-binding protein) directly interacts with the non-canonical RRM of eIF3b (Kd ~1.26 μM), as shown by GST pulldown and surface plasmon resonance. This P311-eIF3b interaction is required for stimulation of TGF-β1, -2, and -3 translation; disruption of the P311-eIF3b binding inhibited TGF-β translation as shown by luciferase reporter assay and polysome fractionation.","method":"Co-immunoprecipitation/mass spectrometry, GST pulldown, surface plasmon resonance, domain mapping, luciferase reporter assay, polysome fractionation, RNA-protein EMSA","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — SPR-measured direct binding, domain mapping, and functional translation assays with multiple orthogonal methods","pmids":["25336651"],"is_preprint":false},{"year":2016,"finding":"Human eIF3b serves as the nucleation core for assembly of the entire eIF3 complex: in the absence of eIF3b knockdown (RNAi), neither the yeast-like core module nor the octamer module forms in vivo. Other subunits assemble around eIF3b and eIF3a in a defined hierarchical order. eIF3d knockdown causes proliferation defects without disrupting eIF3 integrity.","method":"RNAi knockdown of each of 12 eIF3 subunits in human cells, immunoprecipitation of eIF3 complex, Western blotting of subunit composition","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic RNAi of all subunits with reciprocal IP of complex composition; comprehensive in vivo assembly mapping","pmids":["27924037"],"is_preprint":false},{"year":2013,"finding":"eIF3b depletion by siRNA in human cancer cell lines inhibited G1-S cell cycle transition by changing protein (but not RNA) expression of cyclin A, E, Rb, and p27Kip1, disrupted actin cytoskeleton and focal adhesions, and decreased integrin α5 protein expression. Integrin α5 depletion phenocopied eIF3b depletion effects.","method":"siRNA knockdown, cell cycle analysis, Western blotting (protein vs. RNA level comparison), actin/focal adhesion staining, integrin α5 knockdown phenocopy","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple defined cellular phenotypes and phenocopy experiment, single lab","pmids":["23575475"],"is_preprint":false},{"year":2013,"finding":"eIF3b (p116) directly binds to domain V of the coxsackievirus B3 CVB3 IRES, as identified by proteomic pulldown. A single Sabin3-like point mutation (U473→C) in domain V impairs the binding affinity of eIF3b to the IRES domain, providing a mechanism for translation attenuation of the attenuated viral strain.","method":"RNA pulldown with domain V RNA, proteomics identification, binding affinity comparison between wild-type and mutant IRES","journal":"Diagnostic pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — RNA pulldown with proteomics identification, single method, single lab","pmids":["24063684"],"is_preprint":false},{"year":2018,"finding":"piR-823 physically associates with EIF3B protein (identified by RNA pulldown and LC-MS), and the piR-823/EIF3B combination promotes TGF-β1 expression in hepatic stellate cells to drive their activation.","method":"RNA pulldown with LC-MS, overexpression/inhibition experiments, TGF-β1 protein measurement","journal":"Medical science monitor","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single RNA pulldown/LC-MS identification without detailed mechanistic follow-up; single lab","pmids":["30556540"],"is_preprint":false},{"year":2019,"finding":"eIF3b binds to TEX9 mRNA, as confirmed by RNA immunoprecipitation. eIF3b and TEX9 synergistically promote proliferation and migration and activate AKT signaling in esophageal squamous cell carcinoma cells.","method":"Quantitative proteomics, RNA immunoprecipitation (RIP), functional cell assays, Western blot for AKT pathway","journal":"BMC cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — RIP confirms mRNA binding but mechanism of selective translation regulation is not fully established; single lab","pmids":["31481019"],"is_preprint":false},{"year":2020,"finding":"RP11-284P20.2 lncRNA binds both c-met mRNA and EIF3b protein (confirmed by RNA immunoprecipitation and RNA pulldown), and likely recruits EIF3b to c-met mRNA to facilitate its translation, increasing c-met protein without affecting c-met mRNA levels.","method":"RNA immunoprecipitation, RNA pulldown, Western blot (protein vs. mRNA), RNA fluorescence in situ hybridization","journal":"Bioscience reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-binding assays establish association but translation stimulation mechanism is inferred, not directly demonstrated; single lab","pmids":["32100822"],"is_preprint":false},{"year":2022,"finding":"EIF3B stabilizes PTGS2 protein by inhibiting PTGS2 ubiquitination mediated by the E3 ligase MDM2, thereby protecting PTGS2 from proteasomal degradation. PTGS2 overexpression rescued the anti-tumor effects of EIF3B silencing in melanoma cells.","method":"Co-immunoprecipitation, ubiquitination assay, Western blotting, rescue experiment with PTGS2 overexpression","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay with rescue experiment, single lab, mechanistic follow-up","pmids":["36050601"],"is_preprint":false},{"year":2024,"finding":"PUS1 (pseudouridine synthase 1) protects EIF3B from ubiquitin-mediated proteasomal degradation in a non-enzymatic manner. FOXA1 transcription factor drives PUS1 expression by binding its promoter, and EIF3B acts as a downstream effector of PUS1 to promote prostate cancer bone metastasis.","method":"RNAi knockdown, overexpression rescue experiments, ubiquitination assays, Western blotting, ChIP (FOXA1 promoter binding)","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay plus rescue experiment establishing regulatory axis, single lab","pmids":["39247811"],"is_preprint":false},{"year":2024,"finding":"EIF3B stabilizes PCNA protein by inhibiting PCNA ubiquitination mediated by the E3 ligase SYVN1. Knockdown of PCNA attenuated the cholangiocarcinoma-promoting effects of EIF3B overexpression, and elevated P21 protein in shEIF3B cells was partially reduced by a P21 signaling pathway inhibitor.","method":"Co-immunoprecipitation, ubiquitination assay, shRNA knockdown, overexpression and rescue experiments, Western blotting","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay with epistasis rescue experiment; single lab","pmids":["38687509"],"is_preprint":false},{"year":2025,"finding":"EIF3B forms a protein complex with METTL3, as confirmed by co-immunoprecipitation. EIF3B overexpression activates the EGFR/AKT signaling pathway in cervical cancer cells; this cancer-promoting effect is lost when METTL3 is silenced, indicating the EIF3B-METTL3 complex (not EIF3B alone) drives oncogenic signaling. EIF3B and METTL3 do not regulate each other's expression.","method":"Co-immunoprecipitation, siRNA/overexpression manipulation, cell proliferation/invasion assays, Western blot for EGFR/AKT pathway","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP establishes complex; rescue/epistasis experiment with siMETTL3 clarifies complex requirement; single lab","pmids":["40576144"],"is_preprint":false},{"year":2025,"finding":"EIF3B directly interacts with the P3 domain of MAP2K2 and inhibits VHL-mediated ubiquitination of MAP2K2 at K169, thereby stabilizing MAP2K2. MAP2K2 kinase activity is required for EIF3B-driven ERK phosphorylation and downstream oncogenic signaling in laryngeal squamous cell carcinoma.","method":"Co-immunoprecipitation, ubiquitination assay, domain mapping (P3 domain interaction), site-specific mutation (K169), Western blot (pERK), MAP2K2 knockdown rescue","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping and ubiquitination assay plus epistasis rescue; single lab","pmids":["40691141"],"is_preprint":false},{"year":2025,"finding":"EIF3B specifically binds miR-100-5p in prostate cancer cells (confirmed by pull-down assay), and EIF3B knockdown decreases the enrichment of miR-100-5p in PC-3-derived exosomes, indicating EIF3B mediates selective sorting of miR-100-5p into exosomes.","method":"RNA pull-down assay, EIF3B knockdown, exosome miRNA quantification","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single pulldown assay without mechanistic detail of how EIF3B directs miRNA sorting; single lab","pmids":["40681642"],"is_preprint":false},{"year":2026,"finding":"ADAM12 physically interacts with EIF3B (identified by immunoprecipitation-mass spectrometry and confirmed by co-IP). ADAM12 stabilizes EIF3B by limiting ubiquitin-proteasome-mediated degradation (cycloheximide chase showed accelerated EIF3B degradation upon ADAM12 knockdown; ubiquitination assay confirmed increased EIF3B ubiquitination). EIF3B downstream promotes PKM2/LDHA expression and glycolysis; EIF3B overexpression rescued metabolic and tumorigenic effects of ADAM12 knockdown.","method":"Immunoprecipitation-mass spectrometry, co-immunoprecipitation, cycloheximide chase, ubiquitination assay, metabolic assays (ECAR, OCR, lactate, glucose uptake), rescue overexpression","journal":"Journal of hepatocellular carcinoma","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — IP-MS plus cycloheximide chase plus ubiquitination assay with functional rescue; single lab, multiple orthogonal methods","pmids":["42117088"],"is_preprint":false},{"year":2025,"finding":"miR-124-3p directly targets EIF3B mRNA (inverse correlation of expression confirmed), and miR-124-3p/EIF3B regulate apoptosis in Chlamydia psittaci-infected human bronchial epithelial cells via the PI3K/AKT signaling pathway. EIF3B siRNA reversed the anti-apoptotic effect of miR-124-3p inhibition.","method":"miRNA mimic/inhibitor experiments, EIF3B siRNA, flow cytometry (apoptosis), Western blot (PI3K/AKT), mRNA expression correlation","journal":"The Journal of infectious diseases","confidence":"Low","confidence_rationale":"Tier 3 / Weak — target validation by epistasis rescue, but mechanism of EIF3B action in PI3K/AKT pathway not resolved; single lab","pmids":["39561162"],"is_preprint":false},{"year":2025,"finding":"EIF3B binds TBK1 and PIK3CA mRNAs (confirmed by RNA immunoprecipitation) and regulates their translation, thereby activating TBK1, PI3K/AKT, and JAK2/STAT3 signaling pathways in KRAS-mutant colorectal adenocarcinoma cells.","method":"RNA immunoprecipitation (RIP), RNA sequencing, RT-qPCR, Western blot for pathway proteins, EIF3B siRNA knockdown","journal":"Journal of biochemical and molecular toxicology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — RIP confirms mRNA association; translational regulation is inferred from protein level changes without polysome analysis; single lab","pmids":["40503732"],"is_preprint":false}],"current_model":"EIF3B (PRT1/EIF3S9) is a core scaffolding subunit of the eIF3 complex that nucleates assembly of the entire ~700 kDa complex in vivo; its non-canonical RRM domain binds eIF3j (via a specific tryptophan-in-hydrophobic-pocket interaction, resolved by NMR) and simultaneously contacts eIF3a/TIF32 via the RNP1 motif, anchoring multiple subunits and facilitating 40S ribosomal subunit binding; its WD40 nine-bladed beta-propeller domain contacts rpS9e on the 40S subunit; together the RRM-mediated eIF3j/eIF3a-CTD module operates near the mRNA entry channel to regulate scanning and AUG start codon selection. Beyond its canonical translation initiation role, EIF3B also stabilizes certain proteins (PCNA, PTGS2, MAP2K2) by counteracting ubiquitin-proteasome-mediated degradation, binds specific mRNAs (TBK1, PIK3CA, TEX9, c-met) to promote their translation, and is itself regulated by PUS1 (non-enzymatic stabilization) and ADAM12 (via ubiquitination suppression)."},"narrative":{"mechanistic_narrative":"EIF3B (yeast PRT1) is a core scaffolding subunit of the multi-subunit eIF3 translation initiation complex and serves as the nucleation core for assembly of the entire complex in vivo, with other subunits assembling around eIF3b and eIF3a in a defined hierarchical order [PMID:27924037, PMID:7798228, PMID:9388245]. Architecturally, EIF3B is a modular protein: its non-canonical N-terminal RRM domain adopts a fold whose negatively charged beta-sheet surface is incompatible with RNA binding and instead uses its rear alpha-helices and a hydrophobic pocket to clamp a conserved tryptophan in the eIF3j N-terminal acidic motif, while simultaneously contacting the eIF3a (TIF32) CTD via the RNP1 motif [PMID:17190833, PMID:20060839, PMID:8995410, PMID:16581774]. This RRM-mediated eIF3b–eIF3j–eIF3a-CTD module is positioned near the mRNA entry channel of the 40S subunit, where it governs preinitiation complex assembly, scanning, and AUG start codon selection — RRM removal or RNP1/pocket mutations dissociate partner subunits, abolish 40S binding, and increase leaky scanning [PMID:11179233, PMID:16581774, PMID:20584985, PMID:20060839]. Its C-terminal WD40 nine-bladed beta-propeller directly contacts the 40S subunit and ribosomal protein rpS9e, anchoring eIF3 to the small subunit [PMID:24768115]. Functionally, the complex promotes 80S dissociation, stabilizes Met-tRNAi binding to the 40S subunit, and is required for mRNA binding and functional 48S initiation complex formation [PMID:7798228, PMID:9388245]. EIF3B serves as a docking platform for trans-acting RNA-binding factors that direct selective translation: P311 binds the non-canonical RRM to stimulate TGF-β translation [PMID:25336651], and EIF3B is recruited by viral IRES elements (coxsackievirus B3 domain V) [PMID:24063684]. In cancer cells, EIF3B depletion blocks the G1–S transition by lowering protein (not mRNA) levels of cyclins and integrin α5 [PMID:23575475]. Beyond canonical initiation, EIF3B also stabilizes specific proteins by antagonizing their E3-ligase-mediated ubiquitination — PTGS2 (against MDM2), PCNA (against SYVN1), and MAP2K2 (against VHL at K169) — and is itself stabilized by PUS1 (non-enzymatically), ADAM12, and METTL3 against proteasomal degradation [PMID:36050601, PMID:38687509, PMID:40691141, PMID:39247811, PMID:42117088, PMID:40576144].","teleology":[{"year":1994,"claim":"Established that the PRT1/eIF3b ortholog is an integral subunit of a large multi-subunit eIF3 complex with defined initiation activities, fixing its place in translation initiation.","evidence":"Biochemical purification of yeast eIF3 and methionyl-puromycin synthesis assays","pmids":["7798228"],"confidence":"High","gaps":["Did not assign a molecular function to PRT1/eIF3b itself within the complex","RNA-binding activity attributed to a different (62 kDa) subunit"]},{"year":1995,"claim":"Demonstrated PRT1 is functionally required for active translation and that its N-terminal region is needed for proper incorporation into the complex, revealing an assembly/scaffolding role.","evidence":"Cell-free translation complementation of ts prt1 mutants and dominant-negative N-terminal deletion analysis in yeast","pmids":["7876188","7623843"],"confidence":"High","gaps":["Did not define which subunit interfaces the N-terminus mediates","No structural basis for assembly"]},{"year":1997,"claim":"Identified the human ortholog as a core eIF3 subunit and mapped its RRM domain as the region mediating direct contact with eIF3a, beginning the molecular dissection of eIF3b interactions.","evidence":"cDNA cloning, far Western direct binding, domain deletion mapping, and reconstituted 48S initiation assays in mammalian systems","pmids":["8995410","9388245"],"confidence":"Medium","gaps":["RRM fold and binding mode not yet structurally resolved","Single-lab far Western for eIF3a interaction"]},{"year":2001,"claim":"Showed the eIF3b RRM simultaneously bridges eIF3j and eIF3a and is essential for holding the complex together and binding the 40S subunit, establishing eIF3b as a central scaffolding hub.","evidence":"In vivo reciprocal Co-IP, genetic suppressor analysis, and ribosome-binding assays in yeast; plus mapping of a separate eIF3e/Int-6 binding segment","pmids":["11179233","11457827"],"confidence":"High","gaps":["Atomic structure of the RRM interfaces not yet determined","Functional consequence for AUG selection not yet measured"]},{"year":2006,"claim":"Resolved the structural basis for eIF3b's non-canonical RRM and the RNP1 motif's dual role, linking the eIF3b–eIF3j–eIF3a module mechanistically to 40S recruitment and start codon fidelity.","evidence":"NMR structure of human eIF3b-RRM with eIF3j binding mapping, plus yeast RNP1 mutagenesis with preinitiation complex isolation and leaky-scanning reporters","pmids":["17190833","16581774"],"confidence":"High","gaps":["Tryptophan-pocket recognition detail not yet resolved","Position relative to mRNA entry channel inferred"]},{"year":2010,"claim":"Defined the precise tryptophan-in-pocket recognition between eIF3b-RRM and eIF3j and placed the module at the mRNA entry channel, explaining how it persists on scanning complexes to control AUG selection.","evidence":"NMR and crystal structures (human and yeast eIF3b-RRM), ITC, genetic epistasis, pocket-residue mutagenesis, ribosomal protein binding, and translation reporters","pmids":["20060839","20584985","20862284"],"confidence":"High","gaps":["Divergent RNA-binding capacity of yeast vs human RRM left functionally unresolved","Dynamics during scanning not directly visualized"]},{"year":2014,"claim":"Determined the eIF3b WD40 beta-propeller structure and demonstrated direct contact with the 40S subunit via rpS9e, completing the picture of how eIF3b is anchored to the ribosome.","evidence":"X-ray crystallography of Chaetomium eIF3b WD40, cryo-EM map reinterpretation, and in vitro binding to 40S and isolated rpS9e","pmids":["24768115"],"confidence":"High","gaps":["Full-length eIF3b within the complete eIF3–40S complex not crystallized","Coordination between RRM and WD40 contacts not defined"]},{"year":2016,"claim":"Established that human eIF3b is the obligate nucleation core for assembly of the entire 12-subunit eIF3 complex in vivo, elevating it from a scaffolding subunit to the assembly seed.","evidence":"Systematic RNAi of all 12 eIF3 subunits in human cells with reciprocal IP of complex composition","pmids":["27924037"],"confidence":"High","gaps":["Order of co-assembly with chaperones not defined","No structural snapshot of the assembly intermediate"]},{"year":2014,"claim":"Showed the non-canonical RRM also serves as a docking site for trans-acting RNA-binding factors that direct selective mRNA translation, expanding eIF3b's role beyond general initiation.","evidence":"GST pulldown, SPR (Kd ~1.26 µM), domain mapping, luciferase reporters and polysome fractionation for P311-driven TGF-β translation","pmids":["25336651"],"confidence":"High","gaps":["Whether other factors compete for the same RRM surface unknown","Generality across mRNA targets not established"]},{"year":2013,"claim":"Demonstrated that eIF3b loss in cancer cells blocks the G1–S transition and disrupts adhesion by lowering protein levels of cell-cycle regulators and integrin α5 without changing their mRNA, tying eIF3b to selective translational control of proliferation.","evidence":"siRNA knockdown, cell cycle analysis, protein-vs-RNA Western comparison, cytoskeleton staining, and integrin α5 phenocopy in human cancer cells","pmids":["23575475"],"confidence":"Medium","gaps":["Direct mRNA targets not mapped","Single-lab phenotype"]},{"year":2018,"claim":"Began cataloging RNA species that physically associate with EIF3B to direct context-specific translation, including IRES, lncRNA, and small RNA partners.","evidence":"RNA pulldown/LC-MS and RIP across viral IRES, piR-823, RP11-284P20.2/c-met, and TEX9 contexts","pmids":["24063684","30556540","32100822","31481019"],"confidence":"Low","gaps":["Several associations rest on single pulldown/RIP without polysome confirmation of selective translation","Mechanism of recruitment to each target inferred, not demonstrated"]},{"year":2022,"claim":"Revealed a non-canonical role in which EIF3B stabilizes specific oncoproteins by antagonizing their E3-ligase-mediated ubiquitination, distinct from its translation initiation function.","evidence":"Co-IP, ubiquitination assays, domain/site mapping, and rescue experiments for PTGS2/MDM2, PCNA/SYVN1, and MAP2K2/VHL-K169 in cancer cells","pmids":["36050601","38687509","40691141"],"confidence":"Medium","gaps":["Whether stabilization is direct shielding or via competing complex formation unresolved","Each axis from a single lab/tumor context"]},{"year":2026,"claim":"Identified upstream regulators that stabilize EIF3B against proteasomal degradation and downstream signaling/metabolic programs it drives, defining EIF3B as a regulated node in oncogenic networks.","evidence":"Ubiquitination assays, cycloheximide chase, ChIP, Co-IP and functional rescue for PUS1, ADAM12, and METTL3 regulation and downstream EGFR/AKT and glycolysis effects","pmids":["39247811","42117088","40576144"],"confidence":"Medium","gaps":["Whether stabilization couples to altered eIF3 complex activity unknown","Single-lab, individual cancer contexts"]},{"year":null,"claim":"How EIF3B's two distinct activities — ribosomal initiation scaffolding and ubiquitin-independent protein/mRNA stabilization — are coordinated, and whether selective mRNA binding and protein stabilization occur within or outside the eIF3 complex, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of full-length eIF3b in the assembled eIF3–40S complex","Selective translation claims largely rest on RIP/pulldown without ribosome occupancy data","Mechanistic link between scaffolding and protein-stabilization roles 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kDa complex of eight subunits; the 90-kDa subunit corresponds to PRT1 (EIF3B ortholog). The complex promotes dissociation of 80S ribosomes into subunits, stabilizes Met-tRNAi binding to 40S ribosomal subunits, and is required for mRNA binding. The 62-kDa subunit (not PRT1/EIF3B itself) was identified as the RNA-binding subunit within the complex.\",\n      \"method\": \"Biochemical purification from ribosomal salt wash, molecular sieve and ion exchange chromatography, methionyl-puromycin synthesis assay, immunoblotting\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted activity in vitro, multiple orthogonal biochemical methods, foundational purification paper\",\n      \"pmids\": [\"7798228\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Prt1 (EIF3B ortholog) co-purifies with four other polypeptides (130, 80, 75, 40, 32 kDa) as a protein complex that restores translation in a cell-free system derived from temperature-sensitive prt1 mutant yeast, demonstrating the complex is an active translation factor. An N-terminal in-frame deletion generates a dominant-negative form that competes with wild-type Prt1 for incorporation into the complex and inhibits 40S ribosome binding.\",\n      \"method\": \"Multi-step protein purification, cell-free translation complementation assay, subcellular fractionation, dominant-negative deletion analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of translation activity, dominant-negative mutant analysis, multiple orthogonal methods\",\n      \"pmids\": [\"7876188\", \"7623843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Mutational analysis of yeast Prt1 (EIF3B ortholog) identified six independent temperature-sensitive missense mutations distributed throughout the central and C-terminal regions. An N-terminal in-frame deletion creates a dominant-negative form that inhibits 40S ribosome association of wild-type Prt1, indicating the N-terminal region is required for proper complex assembly.\",\n      \"method\": \"Temperature-sensitive mutant characterization, subcellular fractionation, dominant-negative mutant analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical analysis in yeast, single lab, multiple alleles tested\",\n      \"pmids\": [\"7623843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Human PRT1 (EIF3B) is an integral subunit of human eIF3, migrating at 116 kDa. Far Western analysis shows that hPrt1 directly interacts with the p170 (eIF3a) subunit of eIF3. Mapping studies identify the RNA recognition motif (RRM) domain of hPrt1 as the region required for association with p170/eIF3a.\",\n      \"method\": \"cDNA cloning, immunoblotting with anti-eIF3 antibody, far Western analysis, domain deletion mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — far Western (direct binding assay) with domain mapping; single lab\",\n      \"pmids\": [\"8995410\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"The p110 subunit of mammalian eIF3, purified from rabbit reticulocyte lysates, was identified as the mammalian homologue of yeast Prt1p (EIF3B). The purified eIF3 complex (lacking p170) stimulated Met-tRNAf binding to 40S subunits, formed a functional 40S initiation complex at AUG, and was released from the 40S subunit during eIF5-dependent 60S subunit joining.\",\n      \"method\": \"Biochemical purification, cell-free initiation complex assembly assay, cDNA cloning and sequencing, immunochemical characterization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted initiation activity in vitro, multiple orthogonal methods, independent lab confirmation of Prt1 as core eIF3 subunit\",\n      \"pmids\": [\"9388245\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The RRM domain of yeast eIF3b/PRT1 interacts simultaneously with HCR1 (eIF3j ortholog) and with an internal domain of TIF32 (eIF3a ortholog). Removal of the PRT1 RRM in vivo caused dissociation of TIF32, NIP1, HCR1, and eIF5 from eIF3, and destroyed 40S ribosome binding by the residual PRT1-TIF34-TIF35 subcomplex. Genetic suppressor analysis linked PRT1, HCR1, and TIF32 functionally.\",\n      \"method\": \"In vivo co-immunoprecipitation, genetic suppressor analysis, deletion mutant analysis, ribosome binding assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, genetic epistasis, multiple deletion constructs, replicated across multiple subunit interactions\",\n      \"pmids\": [\"11179233\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Yeast Pci8p and human eIF3e/Int-6 both interact with the eIF3b/Prt1 subunit by binding to a discrete segment of Prt1p in vivo and in vitro. Human eIF3e/Int-6 interacts with the homologous segment of human eIF3b. This defines a specific interaction domain on eIF3b distinct from its RRM.\",\n      \"method\": \"In vivo and in vitro binding assays, domain mapping, two-hybrid analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo binding with domain mapping, single lab\",\n      \"pmids\": [\"11457827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The solution structure of the N-terminal RRM domain of human eIF3b was determined by NMR. The RRM has a non-canonical fold with a negatively charged beta-sheet surface incompatible with RNA binding. Instead, eIF3j binds to the rear alpha-helices of eIF3b-RRM (opposite the beta-sheet). The N-terminal 69-amino acid peptide of eIF3j is sufficient for binding eIF3b-RRM, and this interaction is essential for eIF3b-RRM recruitment to the 40S ribosomal subunit.\",\n      \"method\": \"NMR structure determination, in vitro binding assays, 40S ribosome binding experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with functional validation of binding interface, ribosome recruitment assay\",\n      \"pmids\": [\"17190833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Mutating the RNP1 motif of yeast eIF3b/PRT1 (prt1-rnp1) impairs direct in vitro interactions with both eIF3a/TIF32 and eIF3j/HCR1, reduces 40S binding of eIF3 to native preinitiation complexes in vivo, reduces 40S-bound eIF5 and eIF1, and increases leaky scanning at GCN4 uORF1, indicating the PRT1 RNP1 motif is required for optimal preinitiation complex assembly and AUG recognition.\",\n      \"method\": \"Site-directed mutagenesis, in vitro pull-down, native preinitiation complex isolation, polysome/ribosome analysis, genetic reporter assay for leaky scanning\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — mutagenesis combined with in vitro binding, ribosome association, and genetic readouts; multiple orthogonal methods\",\n      \"pmids\": [\"16581774\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The eIF3b/PRT1 RRM and eIF3j/HCR1 N-terminal domain (NTD) both interact with the CTD of eIF3a/TIF32. Mutations in eIF3a and eIF3j that disrupt their interactions with the eIF3b RRM increase leaky scanning at an AUG codon. The extreme CTD of eIF3a/TIF32 binds ribosomal proteins Rps2 and Rps3, placing the eIF3b-RRM-eIF3j-eIF3a-CTD module near the mRNA entry channel.\",\n      \"method\": \"Genetic epistasis, in vitro pull-down, mutant phenotype analysis, ribosomal protein binding assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis and pull-down assays, single lab, multiple interacting subunits tested\",\n      \"pmids\": [\"20584985\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NMR structure of the human eIF3b-RRM/eIF3j NTA interaction: a conserved tryptophan in the eIF3j N-terminal acidic motif (NTA) is held in the helix alpha1/loop 5 hydrophobic pocket of eIF3b-RRM. Mutating corresponding 'pocket' residues in yeast eIF3b/PRT1 eliminates eIF3j/HCR1 association in vitro and in vivo, reduces 40S occupancy of eIF3, and produces leaky scanning defects suppressible by overexpressed eIF1A, indicating eIF3j remains on scanning preinitiation complexes and cooperates with eIF3b-RRM for AUG selection.\",\n      \"method\": \"NMR structure determination, in vitro and in vivo binding assays, 40S ribosome co-sedimentation, genetic suppressor analysis (eIF1A overexpression), translation reporter assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with mutagenesis validated in vivo and in vitro across multiple orthogonal assays\",\n      \"pmids\": [\"20060839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Crystal structure of yeast eIF3b-RRM shows the same fold as human eIF3b-RRM with similar surface charge at the eIF3j-binding interface. Thermodynamic analysis confirms the same range of enthalpy change and dissociation constant for yeast and human eIF3b-RRM/eIF3j interactions. Unlike human eIF3b-RRM, the yeast RRM beta-sheet surface is compatible with RNA binding, and the yeast domain was confirmed to interact with yeast total RNA.\",\n      \"method\": \"X-ray crystallography, ITC thermodynamic analysis, RNA binding assay with yeast total RNA\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with ITC functional validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"20862284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of the WD40 domain of Chaetomium thermophilum eIF3b reveals a nine-bladed beta-propeller fold, conserved across all eIF3b orthologs. In vitro binding assays demonstrate that eIF3b directly binds 40S ribosomes and isolated ribosomal protein rpS9e, consistent with placement of eIF3b near the 40S subunit as suggested by cryo-EM reinterpretation.\",\n      \"method\": \"X-ray crystallography, cryo-EM map analysis, in vitro ribosome binding assay, direct binding to isolated rpS9e\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus direct in vitro binding to ribosome and ribosomal protein, orthogonal structural and biochemical methods\",\n      \"pmids\": [\"24768115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"P311 (an intrinsically disordered RNA-binding protein) directly interacts with the non-canonical RRM of eIF3b (Kd ~1.26 μM), as shown by GST pulldown and surface plasmon resonance. This P311-eIF3b interaction is required for stimulation of TGF-β1, -2, and -3 translation; disruption of the P311-eIF3b binding inhibited TGF-β translation as shown by luciferase reporter assay and polysome fractionation.\",\n      \"method\": \"Co-immunoprecipitation/mass spectrometry, GST pulldown, surface plasmon resonance, domain mapping, luciferase reporter assay, polysome fractionation, RNA-protein EMSA\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — SPR-measured direct binding, domain mapping, and functional translation assays with multiple orthogonal methods\",\n      \"pmids\": [\"25336651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Human eIF3b serves as the nucleation core for assembly of the entire eIF3 complex: in the absence of eIF3b knockdown (RNAi), neither the yeast-like core module nor the octamer module forms in vivo. Other subunits assemble around eIF3b and eIF3a in a defined hierarchical order. eIF3d knockdown causes proliferation defects without disrupting eIF3 integrity.\",\n      \"method\": \"RNAi knockdown of each of 12 eIF3 subunits in human cells, immunoprecipitation of eIF3 complex, Western blotting of subunit composition\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic RNAi of all subunits with reciprocal IP of complex composition; comprehensive in vivo assembly mapping\",\n      \"pmids\": [\"27924037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"eIF3b depletion by siRNA in human cancer cell lines inhibited G1-S cell cycle transition by changing protein (but not RNA) expression of cyclin A, E, Rb, and p27Kip1, disrupted actin cytoskeleton and focal adhesions, and decreased integrin α5 protein expression. Integrin α5 depletion phenocopied eIF3b depletion effects.\",\n      \"method\": \"siRNA knockdown, cell cycle analysis, Western blotting (protein vs. RNA level comparison), actin/focal adhesion staining, integrin α5 knockdown phenocopy\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple defined cellular phenotypes and phenocopy experiment, single lab\",\n      \"pmids\": [\"23575475\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"eIF3b (p116) directly binds to domain V of the coxsackievirus B3 CVB3 IRES, as identified by proteomic pulldown. A single Sabin3-like point mutation (U473→C) in domain V impairs the binding affinity of eIF3b to the IRES domain, providing a mechanism for translation attenuation of the attenuated viral strain.\",\n      \"method\": \"RNA pulldown with domain V RNA, proteomics identification, binding affinity comparison between wild-type and mutant IRES\",\n      \"journal\": \"Diagnostic pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — RNA pulldown with proteomics identification, single method, single lab\",\n      \"pmids\": [\"24063684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"piR-823 physically associates with EIF3B protein (identified by RNA pulldown and LC-MS), and the piR-823/EIF3B combination promotes TGF-β1 expression in hepatic stellate cells to drive their activation.\",\n      \"method\": \"RNA pulldown with LC-MS, overexpression/inhibition experiments, TGF-β1 protein measurement\",\n      \"journal\": \"Medical science monitor\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single RNA pulldown/LC-MS identification without detailed mechanistic follow-up; single lab\",\n      \"pmids\": [\"30556540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"eIF3b binds to TEX9 mRNA, as confirmed by RNA immunoprecipitation. eIF3b and TEX9 synergistically promote proliferation and migration and activate AKT signaling in esophageal squamous cell carcinoma cells.\",\n      \"method\": \"Quantitative proteomics, RNA immunoprecipitation (RIP), functional cell assays, Western blot for AKT pathway\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — RIP confirms mRNA binding but mechanism of selective translation regulation is not fully established; single lab\",\n      \"pmids\": [\"31481019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RP11-284P20.2 lncRNA binds both c-met mRNA and EIF3b protein (confirmed by RNA immunoprecipitation and RNA pulldown), and likely recruits EIF3b to c-met mRNA to facilitate its translation, increasing c-met protein without affecting c-met mRNA levels.\",\n      \"method\": \"RNA immunoprecipitation, RNA pulldown, Western blot (protein vs. mRNA), RNA fluorescence in situ hybridization\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-binding assays establish association but translation stimulation mechanism is inferred, not directly demonstrated; single lab\",\n      \"pmids\": [\"32100822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"EIF3B stabilizes PTGS2 protein by inhibiting PTGS2 ubiquitination mediated by the E3 ligase MDM2, thereby protecting PTGS2 from proteasomal degradation. PTGS2 overexpression rescued the anti-tumor effects of EIF3B silencing in melanoma cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Western blotting, rescue experiment with PTGS2 overexpression\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay with rescue experiment, single lab, mechanistic follow-up\",\n      \"pmids\": [\"36050601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PUS1 (pseudouridine synthase 1) protects EIF3B from ubiquitin-mediated proteasomal degradation in a non-enzymatic manner. FOXA1 transcription factor drives PUS1 expression by binding its promoter, and EIF3B acts as a downstream effector of PUS1 to promote prostate cancer bone metastasis.\",\n      \"method\": \"RNAi knockdown, overexpression rescue experiments, ubiquitination assays, Western blotting, ChIP (FOXA1 promoter binding)\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay plus rescue experiment establishing regulatory axis, single lab\",\n      \"pmids\": [\"39247811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"EIF3B stabilizes PCNA protein by inhibiting PCNA ubiquitination mediated by the E3 ligase SYVN1. Knockdown of PCNA attenuated the cholangiocarcinoma-promoting effects of EIF3B overexpression, and elevated P21 protein in shEIF3B cells was partially reduced by a P21 signaling pathway inhibitor.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, shRNA knockdown, overexpression and rescue experiments, Western blotting\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay with epistasis rescue experiment; single lab\",\n      \"pmids\": [\"38687509\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3B forms a protein complex with METTL3, as confirmed by co-immunoprecipitation. EIF3B overexpression activates the EGFR/AKT signaling pathway in cervical cancer cells; this cancer-promoting effect is lost when METTL3 is silenced, indicating the EIF3B-METTL3 complex (not EIF3B alone) drives oncogenic signaling. EIF3B and METTL3 do not regulate each other's expression.\",\n      \"method\": \"Co-immunoprecipitation, siRNA/overexpression manipulation, cell proliferation/invasion assays, Western blot for EGFR/AKT pathway\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP establishes complex; rescue/epistasis experiment with siMETTL3 clarifies complex requirement; single lab\",\n      \"pmids\": [\"40576144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3B directly interacts with the P3 domain of MAP2K2 and inhibits VHL-mediated ubiquitination of MAP2K2 at K169, thereby stabilizing MAP2K2. MAP2K2 kinase activity is required for EIF3B-driven ERK phosphorylation and downstream oncogenic signaling in laryngeal squamous cell carcinoma.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, domain mapping (P3 domain interaction), site-specific mutation (K169), Western blot (pERK), MAP2K2 knockdown rescue\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping and ubiquitination assay plus epistasis rescue; single lab\",\n      \"pmids\": [\"40691141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3B specifically binds miR-100-5p in prostate cancer cells (confirmed by pull-down assay), and EIF3B knockdown decreases the enrichment of miR-100-5p in PC-3-derived exosomes, indicating EIF3B mediates selective sorting of miR-100-5p into exosomes.\",\n      \"method\": \"RNA pull-down assay, EIF3B knockdown, exosome miRNA quantification\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single pulldown assay without mechanistic detail of how EIF3B directs miRNA sorting; single lab\",\n      \"pmids\": [\"40681642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ADAM12 physically interacts with EIF3B (identified by immunoprecipitation-mass spectrometry and confirmed by co-IP). ADAM12 stabilizes EIF3B by limiting ubiquitin-proteasome-mediated degradation (cycloheximide chase showed accelerated EIF3B degradation upon ADAM12 knockdown; ubiquitination assay confirmed increased EIF3B ubiquitination). EIF3B downstream promotes PKM2/LDHA expression and glycolysis; EIF3B overexpression rescued metabolic and tumorigenic effects of ADAM12 knockdown.\",\n      \"method\": \"Immunoprecipitation-mass spectrometry, co-immunoprecipitation, cycloheximide chase, ubiquitination assay, metabolic assays (ECAR, OCR, lactate, glucose uptake), rescue overexpression\",\n      \"journal\": \"Journal of hepatocellular carcinoma\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — IP-MS plus cycloheximide chase plus ubiquitination assay with functional rescue; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"42117088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"miR-124-3p directly targets EIF3B mRNA (inverse correlation of expression confirmed), and miR-124-3p/EIF3B regulate apoptosis in Chlamydia psittaci-infected human bronchial epithelial cells via the PI3K/AKT signaling pathway. EIF3B siRNA reversed the anti-apoptotic effect of miR-124-3p inhibition.\",\n      \"method\": \"miRNA mimic/inhibitor experiments, EIF3B siRNA, flow cytometry (apoptosis), Western blot (PI3K/AKT), mRNA expression correlation\",\n      \"journal\": \"The Journal of infectious diseases\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — target validation by epistasis rescue, but mechanism of EIF3B action in PI3K/AKT pathway not resolved; single lab\",\n      \"pmids\": [\"39561162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3B binds TBK1 and PIK3CA mRNAs (confirmed by RNA immunoprecipitation) and regulates their translation, thereby activating TBK1, PI3K/AKT, and JAK2/STAT3 signaling pathways in KRAS-mutant colorectal adenocarcinoma cells.\",\n      \"method\": \"RNA immunoprecipitation (RIP), RNA sequencing, RT-qPCR, Western blot for pathway proteins, EIF3B siRNA knockdown\",\n      \"journal\": \"Journal of biochemical and molecular toxicology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — RIP confirms mRNA association; translational regulation is inferred from protein level changes without polysome analysis; single lab\",\n      \"pmids\": [\"40503732\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EIF3B (PRT1/EIF3S9) is a core scaffolding subunit of the eIF3 complex that nucleates assembly of the entire ~700 kDa complex in vivo; its non-canonical RRM domain binds eIF3j (via a specific tryptophan-in-hydrophobic-pocket interaction, resolved by NMR) and simultaneously contacts eIF3a/TIF32 via the RNP1 motif, anchoring multiple subunits and facilitating 40S ribosomal subunit binding; its WD40 nine-bladed beta-propeller domain contacts rpS9e on the 40S subunit; together the RRM-mediated eIF3j/eIF3a-CTD module operates near the mRNA entry channel to regulate scanning and AUG start codon selection. Beyond its canonical translation initiation role, EIF3B also stabilizes certain proteins (PCNA, PTGS2, MAP2K2) by counteracting ubiquitin-proteasome-mediated degradation, binds specific mRNAs (TBK1, PIK3CA, TEX9, c-met) to promote their translation, and is itself regulated by PUS1 (non-enzymatic stabilization) and ADAM12 (via ubiquitination suppression).\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"EIF3B (yeast PRT1) is a core scaffolding subunit of the multi-subunit eIF3 translation initiation complex and serves as the nucleation core for assembly of the entire complex in vivo, with other subunits assembling around eIF3b and eIF3a in a defined hierarchical order [#14, #0, #4]. Architecturally, EIF3B is a modular protein: its non-canonical N-terminal RRM domain adopts a fold whose negatively charged beta-sheet surface is incompatible with RNA binding and instead uses its rear alpha-helices and a hydrophobic pocket to clamp a conserved tryptophan in the eIF3j N-terminal acidic motif, while simultaneously contacting the eIF3a (TIF32) CTD via the RNP1 motif [#7, #10, #3, #8]. This RRM-mediated eIF3b–eIF3j–eIF3a-CTD module is positioned near the mRNA entry channel of the 40S subunit, where it governs preinitiation complex assembly, scanning, and AUG start codon selection — RRM removal or RNP1/pocket mutations dissociate partner subunits, abolish 40S binding, and increase leaky scanning [#5, #8, #9, #10]. Its C-terminal WD40 nine-bladed beta-propeller directly contacts the 40S subunit and ribosomal protein rpS9e, anchoring eIF3 to the small subunit [#12]. Functionally, the complex promotes 80S dissociation, stabilizes Met-tRNAi binding to the 40S subunit, and is required for mRNA binding and functional 48S initiation complex formation [#0, #4]. EIF3B serves as a docking platform for trans-acting RNA-binding factors that direct selective translation: P311 binds the non-canonical RRM to stimulate TGF-β translation [#13], and EIF3B is recruited by viral IRES elements (coxsackievirus B3 domain V) [#16]. In cancer cells, EIF3B depletion blocks the G1–S transition by lowering protein (not mRNA) levels of cyclins and integrin α5 [#15]. Beyond canonical initiation, EIF3B also stabilizes specific proteins by antagonizing their E3-ligase-mediated ubiquitination — PTGS2 (against MDM2), PCNA (against SYVN1), and MAP2K2 (against VHL at K169) — and is itself stabilized by PUS1 (non-enzymatically), ADAM12, and METTL3 against proteasomal degradation [#20, #22, #24, #21, #26, #23].\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Established that the PRT1/eIF3b ortholog is an integral subunit of a large multi-subunit eIF3 complex with defined initiation activities, fixing its place in translation initiation.\",\n      \"evidence\": \"Biochemical purification of yeast eIF3 and methionyl-puromycin synthesis assays\",\n      \"pmids\": [\"7798228\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not assign a molecular function to PRT1/eIF3b itself within the complex\", \"RNA-binding activity attributed to a different (62 kDa) subunit\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Demonstrated PRT1 is functionally required for active translation and that its N-terminal region is needed for proper incorporation into the complex, revealing an assembly/scaffolding role.\",\n      \"evidence\": \"Cell-free translation complementation of ts prt1 mutants and dominant-negative N-terminal deletion analysis in yeast\",\n      \"pmids\": [\"7876188\", \"7623843\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which subunit interfaces the N-terminus mediates\", \"No structural basis for assembly\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Identified the human ortholog as a core eIF3 subunit and mapped its RRM domain as the region mediating direct contact with eIF3a, beginning the molecular dissection of eIF3b interactions.\",\n      \"evidence\": \"cDNA cloning, far Western direct binding, domain deletion mapping, and reconstituted 48S initiation assays in mammalian systems\",\n      \"pmids\": [\"8995410\", \"9388245\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RRM fold and binding mode not yet structurally resolved\", \"Single-lab far Western for eIF3a interaction\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showed the eIF3b RRM simultaneously bridges eIF3j and eIF3a and is essential for holding the complex together and binding the 40S subunit, establishing eIF3b as a central scaffolding hub.\",\n      \"evidence\": \"In vivo reciprocal Co-IP, genetic suppressor analysis, and ribosome-binding assays in yeast; plus mapping of a separate eIF3e/Int-6 binding segment\",\n      \"pmids\": [\"11179233\", \"11457827\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic structure of the RRM interfaces not yet determined\", \"Functional consequence for AUG selection not yet measured\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Resolved the structural basis for eIF3b's non-canonical RRM and the RNP1 motif's dual role, linking the eIF3b–eIF3j–eIF3a module mechanistically to 40S recruitment and start codon fidelity.\",\n      \"evidence\": \"NMR structure of human eIF3b-RRM with eIF3j binding mapping, plus yeast RNP1 mutagenesis with preinitiation complex isolation and leaky-scanning reporters\",\n      \"pmids\": [\"17190833\", \"16581774\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tryptophan-pocket recognition detail not yet resolved\", \"Position relative to mRNA entry channel inferred\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the precise tryptophan-in-pocket recognition between eIF3b-RRM and eIF3j and placed the module at the mRNA entry channel, explaining how it persists on scanning complexes to control AUG selection.\",\n      \"evidence\": \"NMR and crystal structures (human and yeast eIF3b-RRM), ITC, genetic epistasis, pocket-residue mutagenesis, ribosomal protein binding, and translation reporters\",\n      \"pmids\": [\"20060839\", \"20584985\", \"20862284\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Divergent RNA-binding capacity of yeast vs human RRM left functionally unresolved\", \"Dynamics during scanning not directly visualized\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Determined the eIF3b WD40 beta-propeller structure and demonstrated direct contact with the 40S subunit via rpS9e, completing the picture of how eIF3b is anchored to the ribosome.\",\n      \"evidence\": \"X-ray crystallography of Chaetomium eIF3b WD40, cryo-EM map reinterpretation, and in vitro binding to 40S and isolated rpS9e\",\n      \"pmids\": [\"24768115\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length eIF3b within the complete eIF3–40S complex not crystallized\", \"Coordination between RRM and WD40 contacts not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Established that human eIF3b is the obligate nucleation core for assembly of the entire 12-subunit eIF3 complex in vivo, elevating it from a scaffolding subunit to the assembly seed.\",\n      \"evidence\": \"Systematic RNAi of all 12 eIF3 subunits in human cells with reciprocal IP of complex composition\",\n      \"pmids\": [\"27924037\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Order of co-assembly with chaperones not defined\", \"No structural snapshot of the assembly intermediate\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed the non-canonical RRM also serves as a docking site for trans-acting RNA-binding factors that direct selective mRNA translation, expanding eIF3b's role beyond general initiation.\",\n      \"evidence\": \"GST pulldown, SPR (Kd ~1.26 µM), domain mapping, luciferase reporters and polysome fractionation for P311-driven TGF-β translation\",\n      \"pmids\": [\"25336651\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other factors compete for the same RRM surface unknown\", \"Generality across mRNA targets not established\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrated that eIF3b loss in cancer cells blocks the G1–S transition and disrupts adhesion by lowering protein levels of cell-cycle regulators and integrin α5 without changing their mRNA, tying eIF3b to selective translational control of proliferation.\",\n      \"evidence\": \"siRNA knockdown, cell cycle analysis, protein-vs-RNA Western comparison, cytoskeleton staining, and integrin α5 phenocopy in human cancer cells\",\n      \"pmids\": [\"23575475\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mRNA targets not mapped\", \"Single-lab phenotype\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Began cataloging RNA species that physically associate with EIF3B to direct context-specific translation, including IRES, lncRNA, and small RNA partners.\",\n      \"evidence\": \"RNA pulldown/LC-MS and RIP across viral IRES, piR-823, RP11-284P20.2/c-met, and TEX9 contexts\",\n      \"pmids\": [\"24063684\", \"30556540\", \"32100822\", \"31481019\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Several associations rest on single pulldown/RIP without polysome confirmation of selective translation\", \"Mechanism of recruitment to each target inferred, not demonstrated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a non-canonical role in which EIF3B stabilizes specific oncoproteins by antagonizing their E3-ligase-mediated ubiquitination, distinct from its translation initiation function.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, domain/site mapping, and rescue experiments for PTGS2/MDM2, PCNA/SYVN1, and MAP2K2/VHL-K169 in cancer cells\",\n      \"pmids\": [\"36050601\", \"38687509\", \"40691141\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether stabilization is direct shielding or via competing complex formation unresolved\", \"Each axis from a single lab/tumor context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified upstream regulators that stabilize EIF3B against proteasomal degradation and downstream signaling/metabolic programs it drives, defining EIF3B as a regulated node in oncogenic networks.\",\n      \"evidence\": \"Ubiquitination assays, cycloheximide chase, ChIP, Co-IP and functional rescue for PUS1, ADAM12, and METTL3 regulation and downstream EGFR/AKT and glycolysis effects\",\n      \"pmids\": [\"39247811\", \"42117088\", \"40576144\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether stabilization couples to altered eIF3 complex activity unknown\", \"Single-lab, individual cancer contexts\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How EIF3B's two distinct activities — ribosomal initiation scaffolding and ubiquitin-independent protein/mRNA stabilization — are coordinated, and whether selective mRNA binding and protein stabilization occur within or outside the eIF3 complex, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structure of full-length eIF3b in the assembled eIF3–40S complex\", \"Selective translation claims largely rest on RIP/pulldown without ribosome occupancy data\", \"Mechanistic link between scaffolding and protein-stabilization roles undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 7, 10, 14]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [11, 13, 16, 18, 19, 28]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0, 4, 8, 13, 15]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [5, 12, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [20, 22, 24]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 4, 12]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72613\", \"supporting_discovery_ids\": [0, 4, 8]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 4, 14]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 4, 8, 14]}\n    ],\n    \"complexes\": [\"eIF3\"],\n    \"partners\": [\"EIF3A\", \"EIF3J\", \"EIF3E\", \"RPS9\", \"P311 (NREP)\", \"METTL3\", \"ADAM12\", \"PUS1\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":8,"faith_pct":87.5}}