{"gene":"EIF3D","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2016,"finding":"eIF3d possesses a previously unknown cap-binding activity within the 800-kDa eIF3 complex. A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover. eIF3d makes specific contacts with the mRNA 5' cap (validated by cap analogue competition), and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs such as c-Jun. The c-Jun mRNA encodes an inhibitory RNA element that blocks eIF4E recruitment, enforcing alternative cap recognition by eIF3d, defining an eIF4E-independent, cap-dependent translation initiation pathway.","method":"X-ray crystallography (1.4 Å resolution), cap analogue competition assay, in vitro translation initiation complex assembly, mutagenesis","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation (cap analogue competition, mutagenesis, initiation complex assembly) in a single rigorous study; widely replicated conceptually across subsequent papers","pmids":["27462815"],"is_preprint":false},{"year":2020,"finding":"eIF3d cap-binding activity is activated during metabolic stress (glucose deprivation) by reduced CK2-mediated phosphorylation near the eIF3d cap-binding pocket. This phosphorylation switch enables eIF3d to drive selective translation of a gene program enriched in glucose homeostasis factors including mTOR pathway members, and is essential for cell survival during chronic glucose deprivation.","method":"Phosphorylation site mapping, CK2 inhibitor and knockdown experiments, ribosome profiling/translation profiling, cell viability assays under glucose deprivation","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — identified specific kinase (CK2) and phosphorylation site near cap-binding pocket, genome-wide translational profiling, functional rescue; single lab but multiple orthogonal methods and published in high-impact journal","pmids":["33184215"],"is_preprint":false},{"year":2023,"finding":"During persistent integrated stress response (ISR), eIF3d activates translation of the kinase GCN2, which induces eIF2α phosphorylation and inhibits global protein synthesis. In parallel, eIF3d upregulates the m6A demethylase ALKBH5 to drive 5' UTR-specific demethylation of stress response genes including ATF4, increasing ribosome engagement and enhancing bypass of upstream open reading frames (uORFs) on ATF4 mRNA.","method":"Ribosome profiling, m6A sequencing, genetic knockdown/overexpression, uORF reporter assays, eIF2α phosphorylation assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ribosome profiling, m6A-seq, functional reporters), single lab but comprehensive mechanistic dissection","pmids":["37683648"],"is_preprint":false},{"year":2001,"finding":"In fission yeast, Moe1 (homologue of mammalian eIF3d/p66) physically associates with eIF3 core subunits and 40S ribosomal particles as part of an eIF3 complex. Deletion of moe1 reduces translation rate by 30–40% and causes loss of stable association between eIF3 subunits upon ribosome dissociation, demonstrating that eIF3d is required for maintaining eIF3 subunit complex integrity.","method":"Co-immunoprecipitation, sucrose gradient sedimentation, deletion mutant analysis, translation rate measurement","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, fractionation, and functional deletion in yeast ortholog; multiple orthogonal methods","pmids":["11705997"],"is_preprint":false},{"year":2018,"finding":"In Drosophila, eIF3d binds to the msl-2 5' UTR and is required for efficient translation of msl-2 mRNA. eIF3d also mediates translational repression of msl-2 by interacting with the co-factor Hrp48 (which binds the msl-2 3' UTR and is recruited by Sex-lethal). Depletion of eIF3d — but not of other eIF3 subunits — specifically de-represses msl-2 expression in female flies, indicating a subunit-specific role in mRNA-selective translation control.","method":"RNA chromatography, reporter assays, RNAi-mediated depletion in flies, co-immunoprecipitation","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA binding demonstrated by chromatography, functional depletion in vivo, subunit-specificity shown; Drosophila ortholog, single lab","pmids":["29635389"],"is_preprint":false},{"year":2021,"finding":"In human regulatory T cells (Tregs), a non-canonical cap-dependent translation mechanism utilizes DAP5 (eIF4G2) together with eIF3d, directed by 5' noncoding regions of Treg-specific mRNAs, to support translation of Treg differentiation and immune suppression mRNAs when mTORC1/eIF4E-dependent translation is inhibited. Silencing DAP5 impairs naive CD4+ T cell differentiation into Treg cells.","method":"Genome-wide transcriptomic and translatomic profiling, siRNA knockdown, T cell differentiation assays, polysome profiling","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide translatome profiling combined with functional knockdown, single lab","pmids":["34848685"],"is_preprint":false},{"year":2017,"finding":"EIF3D stabilizes GRK2 protein by blocking ubiquitin-mediated proteasomal degradation of GRK2, thereby activating PI3K/Akt signaling and promoting gallbladder cancer cell proliferation and migration. This represents a non-translational function of eIF3d.","method":"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression, in vitro and in vivo proliferation/migration assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and ubiquitination assay supporting interaction and stabilization, single lab with functional follow-up","pmids":["28594409"],"is_preprint":false},{"year":2019,"finding":"EIF3D interacts with GRP78 and enhances GRP78 protein stability by blocking ubiquitin-mediated proteasomal degradation of GRP78, thereby promoting sunitinib resistance in renal cell carcinoma cells via unfolded protein response activation.","method":"Co-immunoprecipitation, Western blot, ubiquitination assay, knockdown/overexpression, in vitro and in vivo growth assays","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal Co-IP and ubiquitination assay demonstrating interaction and stabilization, single lab","pmids":["31669222"],"is_preprint":false},{"year":2019,"finding":"EIF3D is K27-polyubiquitinated at lysine residues K153 and K275 by the Cullin-3/KCTD10 ubiquitin ligase complex in human hepatocellular carcinoma HepG2 cells, as identified by mass spectrometry.","method":"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis of ubiquitination sites, ubiquitination assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — mass spectrometry identification of modification sites plus Co-IP of E3 ligase complex, single lab","pmids":["31280863"],"is_preprint":false},{"year":2022,"finding":"During human cytomegalovirus (HCMV) infection, protein synthesis progressively shifts from eIF4E-dependent to eIF3d-dependent cap-dependent translation. Targeting eIF3d selectively inhibits HCMV replication, reduces polyribosome abundance, and interferes with expression of essential virus genes and a host chronic ER stress gene signature that supports HCMV reproduction.","method":"eIF3d knockdown/targeting, polyribosome profiling, viral replication assays, gene expression analysis","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional knockdown with defined viral and translational phenotype, polyribosome profiling, single lab","pmids":["35508137"],"is_preprint":false},{"year":2023,"finding":"The DAP5/eIF3d complex mediates selective cap-dependent, eIF4E-independent translation of mRNAs encoding EMT transcription factors, cell migration integrins, metalloproteinases, and angiogenesis factors in breast cancer cells. DAP5 is required for EMT, cell migration, invasion, metastasis, and angiogenesis in human and murine breast cancer models, but not for primary tumor growth.","method":"Genome-wide transcriptomic and translatomic profiling, siRNA knockdown, animal models of metastasis, cell migration/invasion assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide translatome profiling plus in vivo metastasis models, single lab","pmids":["37314929"],"is_preprint":false},{"year":2023,"finding":"mTOR inhibition activates eIF3d-mediated non-canonical translation, which cooperates with mRNA-binding proteins hnRNPF, hnRNPK, and SSB to support selective translation of mRNAs in INSR/IGF1R/IRS and IL-6ST/JAK/STAT signaling pathways, enabling cell phenotype switching from proliferative to migratory.","method":"Ribosome profiling, quantitative proteomics, eIF3d knockdown, mTOR inhibitor treatment, co-immunoprecipitation with hnRNPF/K/SSB","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proteomics, ribosome profiling, and Co-IP showing interaction with RBPs; single lab, multiple orthogonal methods","pmids":["37494188"],"is_preprint":false},{"year":2024,"finding":"eIF4E-independent translation of a subset of capped mRNAs is largely dependent on eIF3d cap-binding activity. Under eIF4E1 inactivation, these mRNAs preferentially release eIF4E1 and bind instead to eIF3d via its cap-binding pocket, enabling efficient translation.","method":"Ribosome profiling under constitutively active 4E-BP expression, eIF3d cap-binding pocket mutant, mRNA-eIF3d binding assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — genome-wide ribosome profiling combined with cap-binding pocket mutant and cap-binding assays, mechanistically validates the cap-binding model","pmids":["39107322"],"is_preprint":false},{"year":2025,"finding":"eIF3d and eIF3e mediate a selective translational response to acute hypoxia that controls HIF1α accumulation and cellular invasion. This translation program is dependent on the eIF3d/eIF3e module and can be inhibited by novel small molecules targeting eIF3e.","method":"Ribosome profiling in hypoxia, eIF3d/eIF3e knockdown, cellular invasion assays, HIF1α measurement, small molecule inhibitor characterization","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ribosome profiling plus functional knockdowns with defined molecular phenotypes, single lab","pmids":["41364558"],"is_preprint":false},{"year":2025,"finding":"eIF3d quantitatively recruits itself and the eIF3d/eIF4G2 (DAP5) complex to specific capped mRNAs via its cap-binding activity, with binding affinity dependent on a fully methylated 5' mRNA cap. This eIF3d/eIF4G2 recruitment correlates with translation efficiency of these mRNAs in cap-dependent, eIF4E-independent manner as measured by in vitro translation assays.","method":"Fluorescence anisotropy equilibrium binding assays, in vitro luciferase reporter translation assays, cap analogue competition","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — quantitative in vitro binding assays plus functional translation assay, single lab, first quantitative characterization of eIF3d/eIF4G2 cap recruitment","pmids":["39971159"],"is_preprint":false},{"year":2025,"finding":"EIF3D-mediated translation of ATF4 drives ATF4-dependent S100P transcription in hepatic stellate cells (HSCs), activating JNK and NLRP3 signaling to promote HSC activation, survival, proliferation, and extracellular matrix production. Genetic and pharmacological inhibition of the EIF3D-ATF4-S100P axis suppresses metabolic reprogramming (mitochondrial activity and glycolysis) and fibrogenic markers in HSCs.","method":"Genetic knockdown/overexpression, HSC-specific ATF4 deletion mouse models, pharmacological ISR inhibitor (ERMT1), metabolic assays, fibrosis mouse models","journal":"Redox biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic models plus pharmacological inhibition with multiple fibrosis models; single lab but multiple orthogonal approaches","pmids":["41197183"],"is_preprint":false},{"year":2025,"finding":"EIF3D is required for maintaining primed pluripotency by controlling translation of p53 regulators (keeping p53 activity low) and balancing pluripotency-associated signaling pathways. Loss of EIF3D disrupts this translational homeostasis, compromising the undifferentiated state.","method":"CRISPR interference screen, EIF3D knockdown in human PSCs, ribosome profiling, pluripotency marker analysis","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional CRISPR screen plus ribosome profiling; single lab, defined translational and cellular phenotype","pmids":["40203091"],"is_preprint":false},{"year":2025,"finding":"The RNA-binding domain of eIF3d mediates its recruitment to cytoplasmic stress granules and is required for stress granule assembly in response to specific stresses. Deletion of this domain blocks granule formation, decreases cell viability, and the exogenous RNA-binding domain alone rescues stress granule assembly in eIF3d-depleted cells. This function is conserved in C. elegans.","method":"Live-cell imaging of stress granules, eIF3d domain deletion mutants, eIF3d depletion with rescue, C. elegans in vivo experiments","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain deletion, rescue experiment, conservation in C. elegans; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.11.13.688230"],"is_preprint":true},{"year":2024,"finding":"Src oncogene controls eIF3d-dependent non-canonical cap-dependent translation initiation pathway in addition to the canonical mTOR/eIF4E pathway. eIF3d (together with eIF3h and eIF3e) is essential for invadosome formation and extracellular matrix degradation downstream of Src. Both eIF4E and eIF3d pathways are required for invadosome function.","method":"eIF3d/eIF3h/eIF3e knockdown, invadosome formation assays, ECM degradation assays, Src inhibitor experiments, expression correlation analysis","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional knockdown with invadosome phenotype; preprint, single lab, limited mechanistic detail on direct eIF3d pathway placement","pmids":["bio_10.1101_2024.08.01.606119"],"is_preprint":true}],"current_model":"EIF3D is a subunit of the eIF3 complex that harbors an intrinsic mRNA 5' cap-binding domain (structurally homologous to RNA endonucleases) and functions as the core effector of a non-canonical, eIF4E-independent but cap-dependent translation initiation pathway; its cap-binding activity is regulated by CK2-mediated phosphorylation near the cap-binding pocket, allowing it to be activated during cellular stresses (metabolic, hypoxic, ISR, viral infection) to drive selective translation of specific mRNA programs (including c-Jun, GCN2, ATF4 via m6A/ALKBH5-dependent demethylation, mTOR/glucose homeostasis factors, and hypoxia response genes); eIF3d also functions in a DAP5/eIF4G2 complex for stress- and context-specific translational reprogramming, is required for eIF3 complex subunit stability, is K27-polyubiquitinated at K153/K275 by the CUL3/KCTD10 ligase, and in addition to its translational roles stabilizes certain proteins (GRK2, GRP78) against proteasomal degradation and promotes stress granule assembly via its RNA-binding domain."},"narrative":{"mechanistic_narrative":"EIF3D is the subunit of the eIF3 translation initiation complex that carries an intrinsic mRNA 5' cap-binding domain, defining a non-canonical, eIF4E-independent but cap-dependent pathway of translation initiation [PMID:27462815, PMID:39107322]. Its cap-binding domain is structurally homologous to RNA endonucleases and makes specific contacts with the m7G cap that are required to assemble initiation complexes on specialized mRNAs such as c-Jun, whose 5' inhibitory element blocks eIF4E recruitment [PMID:27462815]; recruitment is quantitatively tuned by full cap methylation and operates on a defined subset of capped mRNAs that release eIF4E and engage eIF3d when eIF4E activity is suppressed [PMID:39107322, PMID:39971159]. This pathway is switched on during cellular stress: glucose deprivation lowers CK2-mediated phosphorylation near the cap-binding pocket to activate eIF3d and drive selective translation of glucose-homeostasis and mTOR-pathway mRNAs essential for survival [PMID:33184215], and during persistent integrated stress response eIF3d activates GCN2 translation and upregulates the m6A demethylase ALKBH5 to enhance ATF4 translation via 5' UTR demethylation and uORF bypass [PMID:37683648]. eIF3d additionally partners with DAP5/eIF4G2 to direct context-specific translational reprogramming of Treg-differentiation, EMT, migration and angiogenesis mRNAs [PMID:34848685, PMID:37314929, PMID:39971159], and the program is engaged downstream of mTOR inhibition, hypoxia (with eIF3e, controlling HIF1α), and viral infection [PMID:37494188, PMID:41364558, PMID:35508137]. As a structural element of the complex, eIF3d is required to maintain eIF3 subunit integrity [PMID:11705997], and beyond translation it stabilizes specific client proteins (GRK2, GRP78) against proteasomal degradation [PMID:28594409, PMID:31669222] and is itself K27-polyubiquitinated at K153/K275 by the CUL3/KCTD10 ligase [PMID:31280863]. Through these activities eIF3d governs selective translational responses controlling fibrogenesis [PMID:41197183] and pluripotency maintenance [PMID:40203091].","teleology":[{"year":2001,"claim":"Established that eIF3d is a physical and functional core component of the eIF3 complex, answering whether it is integral to initiation machinery rather than peripheral.","evidence":"Co-IP, sucrose gradient sedimentation, and moe1 deletion in fission yeast","pmids":["11705997"],"confidence":"High","gaps":["Did not reveal the cap-binding function discovered later","Ortholog-based, mammalian role not directly tested"]},{"year":2016,"claim":"Discovered that eIF3d harbors an intrinsic 5' cap-binding domain, defining an eIF4E-independent yet cap-dependent initiation pathway and explaining mRNA-selective initiation on transcripts like c-Jun.","evidence":"1.4 Å crystal structure, cap analogue competition, mutagenesis, in vitro initiation complex assembly","pmids":["27462815"],"confidence":"High","gaps":["Did not establish how the pathway is regulated in cells","Scope of the eIF3d-dependent mRNA program not defined"]},{"year":2018,"claim":"Demonstrated subunit-specific, mRNA-selective translational control by eIF3d via direct 5' UTR binding and cofactor (Hrp48) interactions, distinguishing its role from other eIF3 subunits.","evidence":"RNA chromatography, reporter assays, RNAi depletion and Co-IP in Drosophila","pmids":["29635389"],"confidence":"Medium","gaps":["Drosophila ortholog, mammalian generality unclear","Direct cap-binding contribution to msl-2 control not dissected"]},{"year":2017,"claim":"Revealed a non-translational function: eIF3d stabilizes client proteins against ubiquitin-mediated degradation, here GRK2 to activate PI3K/Akt in cancer cells.","evidence":"Co-IP, ubiquitination assay, knockdown/overexpression, proliferation/migration assays","pmids":["28594409"],"confidence":"Medium","gaps":["Mechanism of degradation blockade unclear","Direct vs indirect stabilization not resolved"]},{"year":2019,"claim":"Extended the protein-stabilizing role to GRP78 and identified eIF3d as a substrate of CUL3/KCTD10, defining how eIF3d is itself post-translationally regulated.","evidence":"Co-IP, ubiquitination assays, mass spectrometry of K153/K275 sites in cancer cells","pmids":["31669222","31280863"],"confidence":"Medium","gaps":["Functional consequence of K27 ubiquitination on eIF3d activity not established","Reciprocal regulation between translational and stabilizing roles unknown"]},{"year":2020,"claim":"Identified the regulatory switch: CK2 phosphorylation near the cap-binding pocket inhibits eIF3d, and metabolic stress relieves this to activate selective translation, linking the pathway to nutrient sensing and survival.","evidence":"Phosphosite mapping, CK2 inhibition/knockdown, translation profiling, viability assays under glucose deprivation","pmids":["33184215"],"confidence":"High","gaps":["Upstream signaling controlling CK2 in stress not defined","Full breadth of the regulated mRNA program incomplete"]},{"year":2021,"claim":"Showed eIF3d acts with DAP5/eIF4G2 in a distinct complex to support stress/context-specific translation, here Treg differentiation when eIF4E translation is inhibited.","evidence":"Translatome profiling, siRNA knockdown, T cell differentiation and polysome assays","pmids":["34848685"],"confidence":"Medium","gaps":["Direct eIF3d cap-binding contribution within the DAP5 complex not isolated","How target mRNAs are selected unclear"]},{"year":2022,"claim":"Established eIF3d-dependent translation as a host pathway hijacked during HCMV infection as eIF4E activity wanes, identifying it as an antiviral target.","evidence":"eIF3d knockdown, polyribosome profiling, viral replication and gene expression assays","pmids":["35508137"],"confidence":"Medium","gaps":["Viral mRNAs directly bound by eIF3d not mapped","Trigger of the eIF4E-to-eIF3d shift not defined"]},{"year":2023,"claim":"Defined eIF3d as a master coordinator of the integrated stress response by activating GCN2 and ALKBH5-driven m6A demethylation to enhance ATF4 translation, and showed DAP5/eIF3d drives EMT/metastasis programs.","evidence":"Ribosome profiling, m6A-seq, uORF reporters; translatome profiling and metastasis models","pmids":["37683648","37314929","37494188"],"confidence":"High","gaps":["How eIF3d selects ISR and EMT target mRNAs not fully resolved","Interplay with RBP cofactors (hnRNPF/K/SSB) mechanistically incomplete"]},{"year":2024,"claim":"Genome-wide demonstration that eIF4E-independent translation of a defined subset of capped mRNAs is largely dependent on eIF3d cap-binding, mechanistically validating the cap-handoff model.","evidence":"Ribosome profiling under active 4E-BP, cap-binding pocket mutant, mRNA-eIF3d binding assays","pmids":["39107322"],"confidence":"High","gaps":["Determinants of which mRNAs handoff to eIF3d not fully defined","In vivo physiological deployment of the handoff incomplete"]},{"year":2025,"claim":"Quantified cap recruitment of eIF3d/eIF4G2 dependent on full cap methylation and extended eIF3d roles to hypoxia (HIF1α), fibrogenesis (ATF4-S100P axis), pluripotency maintenance, and stress granule assembly via its RNA-binding domain.","evidence":"Fluorescence anisotropy and in vitro translation; ribosome profiling, CRISPRi, fibrosis mouse models, stress granule imaging and domain rescue (one preprint)","pmids":["39971159","41364558","41197183","40203091","bio_10.1101_2025.11.13.688230"],"confidence":"Medium","gaps":["Stress granule role is from a preprint awaiting peer review","Structural basis of RNA-binding-domain-mediated granule assembly not defined"]},{"year":null,"claim":"How the eIF3d cap-binding switch is integrated across competing demands (translation initiation, protein stabilization, stress granule assembly) and how target mRNA selectivity is encoded remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking phosphorylation, ubiquitination, and cofactor binding to target choice","Structural basis for mRNA selectivity beyond the cap unknown","Relative in vivo importance of translational vs non-translational functions unquantified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,4,12,14,17]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[0,1,2,12]},{"term_id":"GO:0140313","term_label":"molecular sequestering activity","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,12,14]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,6,7,8]}],"complexes":["eIF3 complex","DAP5/eIF4G2 (eIF3d) complex"],"partners":["EIF4G2","EIF3E","ALKBH5","GRK2","GRP78","CUL3","KCTD10","HNRNPK"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O15371","full_name":"Eukaryotic translation initiation factor 3 subunit D","aliases":["Eukaryotic translation initiation factor 3 subunit 7","eIF-3-zeta","eIF3 p66"],"length_aa":548,"mass_kda":64.0,"function":"mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, a complex required for several steps in the initiation of protein synthesis of a specialized repertoire of mRNAs (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 (PubMed:18599441, PubMed:25849773). 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). In the eIF-3 complex, EIF3D specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs (PubMed:27462815) (Microbial infection) In case of FCV infection, plays a role in the ribosomal termination-reinitiation event leading to the translation of VP2 (PubMed:18056426)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O15371/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/EIF3D","classification":"Common Essential","n_dependent_lines":1204,"n_total_lines":1208,"dependency_fraction":0.9966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"EIF3B","stoichiometry":10.0},{"gene":"EIF3G","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":4.0},{"gene":"RPS16","stoichiometry":4.0},{"gene":"ATG13","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DDX6","stoichiometry":0.2},{"gene":"SAE1","stoichiometry":0.2},{"gene":"EIF3I","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/EIF3D","total_profiled":1310},"omim":[{"mim_id":"603915","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 3, SUBUNIT D; EIF3D","url":"https://www.omim.org/entry/603915"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/EIF3D"},"hgnc":{"alias_symbol":["eIF3-p66","eIF3-zeta"],"prev_symbol":["EIF3S7"]},"alphafold":{"accession":"O15371","domains":[{"cath_id":"-","chopping":"173-296_304-524","consensus_level":"medium","plddt":95.2248,"start":173,"end":524}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O15371","model_url":"https://alphafold.ebi.ac.uk/files/AF-O15371-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O15371-F1-predicted_aligned_error_v6.png","plddt_mean":82.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EIF3D","jax_strain_url":"https://www.jax.org/strain/search?query=EIF3D"},"sequence":{"accession":"O15371","fasta_url":"https://rest.uniprot.org/uniprotkb/O15371.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O15371/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O15371"}},"corpus_meta":[{"pmid":"27462815","id":"PMC_27462815","title":"eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.","date":"2016","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/27462815","citation_count":292,"is_preprint":false},{"pmid":"33184215","id":"PMC_33184215","title":"A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress.","date":"2020","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/33184215","citation_count":99,"is_preprint":false},{"pmid":"28594409","id":"PMC_28594409","title":"EIF3D promotes gallbladder cancer development by stabilizing GRK2 kinase and activating PI3K-AKT signaling pathway.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/28594409","citation_count":55,"is_preprint":false},{"pmid":"37683648","id":"PMC_37683648","title":"eIF3d controls the persistent integrated stress response.","date":"2023","source":"Molecular 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A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover. eIF3d makes specific contacts with the mRNA 5' cap (validated by cap analogue competition), and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs such as c-Jun. The c-Jun mRNA encodes an inhibitory RNA element that blocks eIF4E recruitment, enforcing alternative cap recognition by eIF3d, defining an eIF4E-independent, cap-dependent translation initiation pathway.\",\n      \"method\": \"X-ray crystallography (1.4 Å resolution), cap analogue competition assay, in vitro translation initiation complex assembly, mutagenesis\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation (cap analogue competition, mutagenesis, initiation complex assembly) in a single rigorous study; widely replicated conceptually across subsequent papers\",\n      \"pmids\": [\"27462815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"eIF3d cap-binding activity is activated during metabolic stress (glucose deprivation) by reduced CK2-mediated phosphorylation near the eIF3d cap-binding pocket. This phosphorylation switch enables eIF3d to drive selective translation of a gene program enriched in glucose homeostasis factors including mTOR pathway members, and is essential for cell survival during chronic glucose deprivation.\",\n      \"method\": \"Phosphorylation site mapping, CK2 inhibitor and knockdown experiments, ribosome profiling/translation profiling, cell viability assays under glucose deprivation\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — identified specific kinase (CK2) and phosphorylation site near cap-binding pocket, genome-wide translational profiling, functional rescue; single lab but multiple orthogonal methods and published in high-impact journal\",\n      \"pmids\": [\"33184215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"During persistent integrated stress response (ISR), eIF3d activates translation of the kinase GCN2, which induces eIF2α phosphorylation and inhibits global protein synthesis. In parallel, eIF3d upregulates the m6A demethylase ALKBH5 to drive 5' UTR-specific demethylation of stress response genes including ATF4, increasing ribosome engagement and enhancing bypass of upstream open reading frames (uORFs) on ATF4 mRNA.\",\n      \"method\": \"Ribosome profiling, m6A sequencing, genetic knockdown/overexpression, uORF reporter assays, eIF2α phosphorylation assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ribosome profiling, m6A-seq, functional reporters), single lab but comprehensive mechanistic dissection\",\n      \"pmids\": [\"37683648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"In fission yeast, Moe1 (homologue of mammalian eIF3d/p66) physically associates with eIF3 core subunits and 40S ribosomal particles as part of an eIF3 complex. Deletion of moe1 reduces translation rate by 30–40% and causes loss of stable association between eIF3 subunits upon ribosome dissociation, demonstrating that eIF3d is required for maintaining eIF3 subunit complex integrity.\",\n      \"method\": \"Co-immunoprecipitation, sucrose gradient sedimentation, deletion mutant analysis, translation rate measurement\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, fractionation, and functional deletion in yeast ortholog; multiple orthogonal methods\",\n      \"pmids\": [\"11705997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In Drosophila, eIF3d binds to the msl-2 5' UTR and is required for efficient translation of msl-2 mRNA. eIF3d also mediates translational repression of msl-2 by interacting with the co-factor Hrp48 (which binds the msl-2 3' UTR and is recruited by Sex-lethal). Depletion of eIF3d — but not of other eIF3 subunits — specifically de-represses msl-2 expression in female flies, indicating a subunit-specific role in mRNA-selective translation control.\",\n      \"method\": \"RNA chromatography, reporter assays, RNAi-mediated depletion in flies, co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA binding demonstrated by chromatography, functional depletion in vivo, subunit-specificity shown; Drosophila ortholog, single lab\",\n      \"pmids\": [\"29635389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In human regulatory T cells (Tregs), a non-canonical cap-dependent translation mechanism utilizes DAP5 (eIF4G2) together with eIF3d, directed by 5' noncoding regions of Treg-specific mRNAs, to support translation of Treg differentiation and immune suppression mRNAs when mTORC1/eIF4E-dependent translation is inhibited. Silencing DAP5 impairs naive CD4+ T cell differentiation into Treg cells.\",\n      \"method\": \"Genome-wide transcriptomic and translatomic profiling, siRNA knockdown, T cell differentiation assays, polysome profiling\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide translatome profiling combined with functional knockdown, single lab\",\n      \"pmids\": [\"34848685\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"EIF3D stabilizes GRK2 protein by blocking ubiquitin-mediated proteasomal degradation of GRK2, thereby activating PI3K/Akt signaling and promoting gallbladder cancer cell proliferation and migration. This represents a non-translational function of eIF3d.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression, in vitro and in vivo proliferation/migration assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and ubiquitination assay supporting interaction and stabilization, single lab with functional follow-up\",\n      \"pmids\": [\"28594409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"EIF3D interacts with GRP78 and enhances GRP78 protein stability by blocking ubiquitin-mediated proteasomal degradation of GRP78, thereby promoting sunitinib resistance in renal cell carcinoma cells via unfolded protein response activation.\",\n      \"method\": \"Co-immunoprecipitation, Western blot, ubiquitination assay, knockdown/overexpression, in vitro and in vivo growth assays\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal Co-IP and ubiquitination assay demonstrating interaction and stabilization, single lab\",\n      \"pmids\": [\"31669222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"EIF3D is K27-polyubiquitinated at lysine residues K153 and K275 by the Cullin-3/KCTD10 ubiquitin ligase complex in human hepatocellular carcinoma HepG2 cells, as identified by mass spectrometry.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis of ubiquitination sites, ubiquitination assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mass spectrometry identification of modification sites plus Co-IP of E3 ligase complex, single lab\",\n      \"pmids\": [\"31280863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"During human cytomegalovirus (HCMV) infection, protein synthesis progressively shifts from eIF4E-dependent to eIF3d-dependent cap-dependent translation. Targeting eIF3d selectively inhibits HCMV replication, reduces polyribosome abundance, and interferes with expression of essential virus genes and a host chronic ER stress gene signature that supports HCMV reproduction.\",\n      \"method\": \"eIF3d knockdown/targeting, polyribosome profiling, viral replication assays, gene expression analysis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional knockdown with defined viral and translational phenotype, polyribosome profiling, single lab\",\n      \"pmids\": [\"35508137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The DAP5/eIF3d complex mediates selective cap-dependent, eIF4E-independent translation of mRNAs encoding EMT transcription factors, cell migration integrins, metalloproteinases, and angiogenesis factors in breast cancer cells. DAP5 is required for EMT, cell migration, invasion, metastasis, and angiogenesis in human and murine breast cancer models, but not for primary tumor growth.\",\n      \"method\": \"Genome-wide transcriptomic and translatomic profiling, siRNA knockdown, animal models of metastasis, cell migration/invasion assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide translatome profiling plus in vivo metastasis models, single lab\",\n      \"pmids\": [\"37314929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"mTOR inhibition activates eIF3d-mediated non-canonical translation, which cooperates with mRNA-binding proteins hnRNPF, hnRNPK, and SSB to support selective translation of mRNAs in INSR/IGF1R/IRS and IL-6ST/JAK/STAT signaling pathways, enabling cell phenotype switching from proliferative to migratory.\",\n      \"method\": \"Ribosome profiling, quantitative proteomics, eIF3d knockdown, mTOR inhibitor treatment, co-immunoprecipitation with hnRNPF/K/SSB\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteomics, ribosome profiling, and Co-IP showing interaction with RBPs; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37494188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"eIF4E-independent translation of a subset of capped mRNAs is largely dependent on eIF3d cap-binding activity. Under eIF4E1 inactivation, these mRNAs preferentially release eIF4E1 and bind instead to eIF3d via its cap-binding pocket, enabling efficient translation.\",\n      \"method\": \"Ribosome profiling under constitutively active 4E-BP expression, eIF3d cap-binding pocket mutant, mRNA-eIF3d binding assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — genome-wide ribosome profiling combined with cap-binding pocket mutant and cap-binding assays, mechanistically validates the cap-binding model\",\n      \"pmids\": [\"39107322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"eIF3d and eIF3e mediate a selective translational response to acute hypoxia that controls HIF1α accumulation and cellular invasion. This translation program is dependent on the eIF3d/eIF3e module and can be inhibited by novel small molecules targeting eIF3e.\",\n      \"method\": \"Ribosome profiling in hypoxia, eIF3d/eIF3e knockdown, cellular invasion assays, HIF1α measurement, small molecule inhibitor characterization\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ribosome profiling plus functional knockdowns with defined molecular phenotypes, single lab\",\n      \"pmids\": [\"41364558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"eIF3d quantitatively recruits itself and the eIF3d/eIF4G2 (DAP5) complex to specific capped mRNAs via its cap-binding activity, with binding affinity dependent on a fully methylated 5' mRNA cap. This eIF3d/eIF4G2 recruitment correlates with translation efficiency of these mRNAs in cap-dependent, eIF4E-independent manner as measured by in vitro translation assays.\",\n      \"method\": \"Fluorescence anisotropy equilibrium binding assays, in vitro luciferase reporter translation assays, cap analogue competition\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — quantitative in vitro binding assays plus functional translation assay, single lab, first quantitative characterization of eIF3d/eIF4G2 cap recruitment\",\n      \"pmids\": [\"39971159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3D-mediated translation of ATF4 drives ATF4-dependent S100P transcription in hepatic stellate cells (HSCs), activating JNK and NLRP3 signaling to promote HSC activation, survival, proliferation, and extracellular matrix production. Genetic and pharmacological inhibition of the EIF3D-ATF4-S100P axis suppresses metabolic reprogramming (mitochondrial activity and glycolysis) and fibrogenic markers in HSCs.\",\n      \"method\": \"Genetic knockdown/overexpression, HSC-specific ATF4 deletion mouse models, pharmacological ISR inhibitor (ERMT1), metabolic assays, fibrosis mouse models\",\n      \"journal\": \"Redox biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic models plus pharmacological inhibition with multiple fibrosis models; single lab but multiple orthogonal approaches\",\n      \"pmids\": [\"41197183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EIF3D is required for maintaining primed pluripotency by controlling translation of p53 regulators (keeping p53 activity low) and balancing pluripotency-associated signaling pathways. Loss of EIF3D disrupts this translational homeostasis, compromising the undifferentiated state.\",\n      \"method\": \"CRISPR interference screen, EIF3D knockdown in human PSCs, ribosome profiling, pluripotency marker analysis\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional CRISPR screen plus ribosome profiling; single lab, defined translational and cellular phenotype\",\n      \"pmids\": [\"40203091\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The RNA-binding domain of eIF3d mediates its recruitment to cytoplasmic stress granules and is required for stress granule assembly in response to specific stresses. Deletion of this domain blocks granule formation, decreases cell viability, and the exogenous RNA-binding domain alone rescues stress granule assembly in eIF3d-depleted cells. This function is conserved in C. elegans.\",\n      \"method\": \"Live-cell imaging of stress granules, eIF3d domain deletion mutants, eIF3d depletion with rescue, C. elegans in vivo experiments\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain deletion, rescue experiment, conservation in C. elegans; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.11.13.688230\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Src oncogene controls eIF3d-dependent non-canonical cap-dependent translation initiation pathway in addition to the canonical mTOR/eIF4E pathway. eIF3d (together with eIF3h and eIF3e) is essential for invadosome formation and extracellular matrix degradation downstream of Src. Both eIF4E and eIF3d pathways are required for invadosome function.\",\n      \"method\": \"eIF3d/eIF3h/eIF3e knockdown, invadosome formation assays, ECM degradation assays, Src inhibitor experiments, expression correlation analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional knockdown with invadosome phenotype; preprint, single lab, limited mechanistic detail on direct eIF3d pathway placement\",\n      \"pmids\": [\"bio_10.1101_2024.08.01.606119\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"EIF3D is a subunit of the eIF3 complex that harbors an intrinsic mRNA 5' cap-binding domain (structurally homologous to RNA endonucleases) and functions as the core effector of a non-canonical, eIF4E-independent but cap-dependent translation initiation pathway; its cap-binding activity is regulated by CK2-mediated phosphorylation near the cap-binding pocket, allowing it to be activated during cellular stresses (metabolic, hypoxic, ISR, viral infection) to drive selective translation of specific mRNA programs (including c-Jun, GCN2, ATF4 via m6A/ALKBH5-dependent demethylation, mTOR/glucose homeostasis factors, and hypoxia response genes); eIF3d also functions in a DAP5/eIF4G2 complex for stress- and context-specific translational reprogramming, is required for eIF3 complex subunit stability, is K27-polyubiquitinated at K153/K275 by the CUL3/KCTD10 ligase, and in addition to its translational roles stabilizes certain proteins (GRK2, GRP78) against proteasomal degradation and promotes stress granule assembly via its RNA-binding domain.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EIF3D is the subunit of the eIF3 translation initiation complex that carries an intrinsic mRNA 5' cap-binding domain, defining a non-canonical, eIF4E-independent but cap-dependent pathway of translation initiation [#0, #12]. Its cap-binding domain is structurally homologous to RNA endonucleases and makes specific contacts with the m7G cap that are required to assemble initiation complexes on specialized mRNAs such as c-Jun, whose 5' inhibitory element blocks eIF4E recruitment [#0]; recruitment is quantitatively tuned by full cap methylation and operates on a defined subset of capped mRNAs that release eIF4E and engage eIF3d when eIF4E activity is suppressed [#12, #14]. This pathway is switched on during cellular stress: glucose deprivation lowers CK2-mediated phosphorylation near the cap-binding pocket to activate eIF3d and drive selective translation of glucose-homeostasis and mTOR-pathway mRNAs essential for survival [#1], and during persistent integrated stress response eIF3d activates GCN2 translation and upregulates the m6A demethylase ALKBH5 to enhance ATF4 translation via 5' UTR demethylation and uORF bypass [#2]. eIF3d additionally partners with DAP5/eIF4G2 to direct context-specific translational reprogramming of Treg-differentiation, EMT, migration and angiogenesis mRNAs [#5, #10, #14], and the program is engaged downstream of mTOR inhibition, hypoxia (with eIF3e, controlling HIF1\\u03b1), and viral infection [#11, #13, #9]. As a structural element of the complex, eIF3d is required to maintain eIF3 subunit integrity [#3], and beyond translation it stabilizes specific client proteins (GRK2, GRP78) against proteasomal degradation [#6, #7] and is itself K27-polyubiquitinated at K153/K275 by the CUL3/KCTD10 ligase [#8]. Through these activities eIF3d governs selective translational responses controlling fibrogenesis [#15] and pluripotency maintenance [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that eIF3d is a physical and functional core component of the eIF3 complex, answering whether it is integral to initiation machinery rather than peripheral.\",\n      \"evidence\": \"Co-IP, sucrose gradient sedimentation, and moe1 deletion in fission yeast\",\n      \"pmids\": [\"11705997\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not reveal the cap-binding function discovered later\", \"Ortholog-based, mammalian role not directly tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Discovered that eIF3d harbors an intrinsic 5' cap-binding domain, defining an eIF4E-independent yet cap-dependent initiation pathway and explaining mRNA-selective initiation on transcripts like c-Jun.\",\n      \"evidence\": \"1.4 \\u00c5 crystal structure, cap analogue competition, mutagenesis, in vitro initiation complex assembly\",\n      \"pmids\": [\"27462815\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish how the pathway is regulated in cells\", \"Scope of the eIF3d-dependent mRNA program not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated subunit-specific, mRNA-selective translational control by eIF3d via direct 5' UTR binding and cofactor (Hrp48) interactions, distinguishing its role from other eIF3 subunits.\",\n      \"evidence\": \"RNA chromatography, reporter assays, RNAi depletion and Co-IP in Drosophila\",\n      \"pmids\": [\"29635389\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Drosophila ortholog, mammalian generality unclear\", \"Direct cap-binding contribution to msl-2 control not dissected\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed a non-translational function: eIF3d stabilizes client proteins against ubiquitin-mediated degradation, here GRK2 to activate PI3K/Akt in cancer cells.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, knockdown/overexpression, proliferation/migration assays\",\n      \"pmids\": [\"28594409\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of degradation blockade unclear\", \"Direct vs indirect stabilization not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended the protein-stabilizing role to GRP78 and identified eIF3d as a substrate of CUL3/KCTD10, defining how eIF3d is itself post-translationally regulated.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, mass spectrometry of K153/K275 sites in cancer cells\",\n      \"pmids\": [\"31669222\", \"31280863\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of K27 ubiquitination on eIF3d activity not established\", \"Reciprocal regulation between translational and stabilizing roles unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified the regulatory switch: CK2 phosphorylation near the cap-binding pocket inhibits eIF3d, and metabolic stress relieves this to activate selective translation, linking the pathway to nutrient sensing and survival.\",\n      \"evidence\": \"Phosphosite mapping, CK2 inhibition/knockdown, translation profiling, viability assays under glucose deprivation\",\n      \"pmids\": [\"33184215\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signaling controlling CK2 in stress not defined\", \"Full breadth of the regulated mRNA program incomplete\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed eIF3d acts with DAP5/eIF4G2 in a distinct complex to support stress/context-specific translation, here Treg differentiation when eIF4E translation is inhibited.\",\n      \"evidence\": \"Translatome profiling, siRNA knockdown, T cell differentiation and polysome assays\",\n      \"pmids\": [\"34848685\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct eIF3d cap-binding contribution within the DAP5 complex not isolated\", \"How target mRNAs are selected unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established eIF3d-dependent translation as a host pathway hijacked during HCMV infection as eIF4E activity wanes, identifying it as an antiviral target.\",\n      \"evidence\": \"eIF3d knockdown, polyribosome profiling, viral replication and gene expression assays\",\n      \"pmids\": [\"35508137\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Viral mRNAs directly bound by eIF3d not mapped\", \"Trigger of the eIF4E-to-eIF3d shift not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined eIF3d as a master coordinator of the integrated stress response by activating GCN2 and ALKBH5-driven m6A demethylation to enhance ATF4 translation, and showed DAP5/eIF3d drives EMT/metastasis programs.\",\n      \"evidence\": \"Ribosome profiling, m6A-seq, uORF reporters; translatome profiling and metastasis models\",\n      \"pmids\": [\"37683648\", \"37314929\", \"37494188\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How eIF3d selects ISR and EMT target mRNAs not fully resolved\", \"Interplay with RBP cofactors (hnRNPF/K/SSB) mechanistically incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genome-wide demonstration that eIF4E-independent translation of a defined subset of capped mRNAs is largely dependent on eIF3d cap-binding, mechanistically validating the cap-handoff model.\",\n      \"evidence\": \"Ribosome profiling under active 4E-BP, cap-binding pocket mutant, mRNA-eIF3d binding assays\",\n      \"pmids\": [\"39107322\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of which mRNAs handoff to eIF3d not fully defined\", \"In vivo physiological deployment of the handoff incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Quantified cap recruitment of eIF3d/eIF4G2 dependent on full cap methylation and extended eIF3d roles to hypoxia (HIF1\\u03b1), fibrogenesis (ATF4-S100P axis), pluripotency maintenance, and stress granule assembly via its RNA-binding domain.\",\n      \"evidence\": \"Fluorescence anisotropy and in vitro translation; ribosome profiling, CRISPRi, fibrosis mouse models, stress granule imaging and domain rescue (one preprint)\",\n      \"pmids\": [\"39971159\", \"41364558\", \"41197183\", \"40203091\", \"bio_10.1101_2025.11.13.688230\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stress granule role is from a preprint awaiting peer review\", \"Structural basis of RNA-binding-domain-mediated granule assembly not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the eIF3d cap-binding switch is integrated across competing demands (translation initiation, protein stabilization, stress granule assembly) and how target mRNA selectivity is encoded remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking phosphorylation, ubiquitination, and cofactor binding to target choice\", \"Structural basis for mRNA selectivity beyond the cap unknown\", \"Relative in vivo importance of translational vs non-translational functions unquantified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 4, 12, 14, 17]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0, 1, 2, 12]},\n      {\"term_id\": \"GO:0140313\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [0, 12]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 12, 14]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 6, 7, 8]}\n    ],\n    \"complexes\": [\n      \"eIF3 complex\",\n      \"DAP5/eIF4G2 (eIF3d) complex\"\n    ],\n    \"partners\": [\n      \"EIF4G2\",\n      \"EIF3E\",\n      \"ALKBH5\",\n      \"GRK2\",\n      \"GRP78\",\n      \"CUL3\",\n      \"KCTD10\",\n      \"hnRNPK\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}