{"gene":"EIF2D","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2017,"finding":"Crystal structure of the C-terminal domains of human eIF2D determined at 1.4-Å resolution, revealing one domain with a fold similar to eIF1 (important for scanning and initiation codon selection) and a second domain with a SWIB/MDM2 fold not previously observed in translation initiation factors, with atomic details of inter-domain interactions.","method":"X-ray crystallography","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure at 1.4-Å resolution with domain-fold assignments; single study but high-resolution structural data","pmids":["28736176"],"is_preprint":false},{"year":2018,"finding":"Yeast Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S ribosomal subunit recycling factors in vivo at stop codons; deletion strains showed 80S ribosomes queued behind stop codons, unrecycled ribosomes reinitiated at 3' UTR AUG codons, and in vitro translation experiments confirmed increased reinitiation at uORFs in their absence.","method":"Ribosome profiling of deletion strains, 3' UTR reporter analysis, in vitro translation assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — ribosome profiling combined with in vitro translation and reporter assays, replicated across multiple deletion strains and methods","pmids":["30146315"],"is_preprint":false},{"year":2018,"finding":"eIF2D and eIF2A are NOT required for translation of Sindbis virus subgenomic mRNA under conditions of eIF2α phosphorylation; CRISPR/Cas9 knockout of eIF2D in HAP1 cells showed comparable viral protein synthesis to wild-type cells.","method":"CRISPR/Cas9 knockout cell lines, viral infection and protein synthesis assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined functional readout, but single lab; negative finding confirmed by siRNA knockdown as well","pmids":["28240315"],"is_preprint":false},{"year":2018,"finding":"eIF2D and eIF2A are NOT required for HCV IRES-driven translation in human cells; HAP1 cells depleted for eIF2D (individually or combined with eIF2A) synthesized luciferase from HCV IRES-bearing mRNA even when eIF2α was phosphorylated.","method":"HAP1 knockout cell lines, IRES-reporter luciferase assay","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with functional reporter assay, single lab; negative result confirmed across multiple conditions","pmids":["29487587"],"is_preprint":false},{"year":2018,"finding":"Translation of the eIF2D mRNA itself is selectively downregulated during hyperosmotic stress via a novel uORF-based regulatory mechanism dependent on events at the uORF stop codon or immediately downstream, distinct from delayed reinitiation, altered AUG recognition, ribosome stalling, or mRNA destabilization.","method":"Reporter mRNA assays, fleeting mRNA transfection (FLERT) technique with mutational analysis of uORF elements","journal":"Biochimie","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple reporter constructs and FLERT technique in single lab with mechanistic dissection","pmids":["30419262"],"is_preprint":false},{"year":2020,"finding":"eIF2D and DENR are critical mediators of ATF4 translational induction during the integrated stress response; loss of eIF2D and DENR in Drosophila phenocopies ATF4 mutants, and eIF2D requires its RNA-binding motif for regulation of 5' leader-mediated ATF4 translation. eIF2D/DENR-deficient human cells show impaired ATF4 protein induction in response to ER stress.","method":"Drosophila genetic loss-of-function, domain mutational analysis (RNA-binding motif), human cell knockdown with ATF4 protein induction assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis in Drosophila, domain mutagenesis, and human cell validation across multiple stress conditions","pmids":["32938929"],"is_preprint":false},{"year":2021,"finding":"40S ribosome footprinting directly demonstrated that deletion of TMA64 (eIF2D) leads to accumulation of unrecycled 40S subunits at stop codons; however, the Tma20/Tma22 (MCT-1/DENR) heterodimer was responsible for the majority of 40S recycling events, while Tma64 played a minor role.","method":"40S ribosome footprinting (selective ribosome profiling) in deletion strains","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct footprinting of recycling intermediates with multiple deletion strains; replicated and extended earlier findings","pmids":["34016977"],"is_preprint":false},{"year":2021,"finding":"eIF2D (eif-2D) promotes repeat-associated non-AUG (RAN) translation of C9orf72 GGGGCC repeat expansions; loss-of-function mutations in eif-2D in C. elegans reduced poly-GA and poly-GP dipeptide repeat protein levels and increased lifespan in disease models. In vitro studies in mammalian cells yielded similar results, establishing a conserved role for eIF2D in DPR expression.","method":"C. elegans loss-of-function genetics, mammalian cell in vitro studies, lifespan assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function in C. elegans plus mammalian cell validation, multiple DPR species measured across two independent model systems","pmids":["34654821"],"is_preprint":false},{"year":2023,"finding":"eIF2D (together with eIF2A) is required for IRES-independent translation of the enterovirus genome under conditions in which the eIF2-dependent mechanism is inactive; this noncanonical mechanism supports sufficient translation of nonstructural regions to permit genome recombination.","method":"Genetic depletion of eIF2A/eIF2D, viral replication and recombination assays, translation reporters","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional depletion experiments with viral replication readout, single lab, two factors tested together making individual contributions unclear","pmids":["36689548"],"is_preprint":false},{"year":2025,"finding":"eIF2D promotes 40S ribosomal subunit recycling specifically during intrinsic ribosome destabilization (IRD), a process occurring when ribosomes translate proteins with consecutive acidic amino acids at their N-terminus. Selective translation complex profiling (TCP-seq) showed eIF2D preferentially associates with IRD-prone regions. The winged helix domain unique to eIF2D (absent in MCTS1-DENR) enhances binding to 40S subunits but likely clashes with ABCE1 during stop-codon-associated recycling, explaining mechanistic divergence from MCTS1-DENR.","method":"TCP-seq (selective translation complex profiling), eIF2D-deficient cells, domain structure-function analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — TCP-seq profiling with domain mutational analysis and functional readout in KO cells; single lab with multiple orthogonal methods","pmids":["41335470"],"is_preprint":false},{"year":2025,"finding":"Knockdown of eIF2D causes widespread gene deregulation unrelated to uORF translation, distinguishing its function from MCTS1-DENR-dependent re-initiation regulation; in cell-free re-initiation assays using HeLa lysates, eIF2D's role in re-initiation at specific uORFs was found to be distinct from that of MCTS1-DENR.","method":"Cell-free re-initiation assay (HeLa lysates), ribosome profiling in knockdown cells, uORF reporters","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro reconstitution assay combined with ribosome profiling and knockdown, single lab","pmids":["39748120"],"is_preprint":false}],"current_model":"eIF2D is a noncanonical translation initiation factor whose C-terminal region contains an eIF1-like domain and a SWIB/MDM2 domain; it promotes 40S ribosomal subunit recycling (particularly during intrinsic ribosome destabilization via its unique winged helix domain), mediates translation reinitiation at upstream ORFs, drives ATF4 translational induction during integrated stress response through its RNA-binding motif, supports RAN translation of C9orf72 repeat expansions, and enables IRES-independent translation of enteroviral genomes — while being dispensable for HCV IRES-driven and Sindbis virus subgenomic mRNA translation."},"narrative":{"mechanistic_narrative":"eIF2D is a noncanonical translation factor that acts at the interface of 40S ribosomal subunit recycling and reinitiation, governing the post-termination and noncanonical-initiation fates of ribosomes [PMID:30146315, PMID:34016977]. Structurally it pairs an eIF1-like domain (linked to scanning and initiation codon selection) with a SWIB/MDM2 fold not previously seen among initiation factors, providing the architecture for its dual roles [PMID:28736176]. In yeast and in 40S footprinting assays, eIF2D (Tma64) recycles 40S subunits stranded at stop codons, preventing aberrant reinitiation at downstream AUG and 3' UTR codons, although the MCT-1/DENR heterodimer carries the bulk of canonical stop-codon recycling and eIF2D plays a comparatively minor role there [PMID:30146315, PMID:34016977]. eIF2D's mechanistic specialization is its winged helix domain, absent from MCTS1-DENR, which enhances 40S binding and directs eIF2D toward recycling during intrinsic ribosome destabilization at nascent N-terminal acidic stretches, a context where it would clash with ABCE1 in conventional termination-coupled recycling [PMID:41335470]. Through these activities eIF2D supports specialized translation programs: it mediates ATF4 translational induction during the integrated stress response via its RNA-binding motif and 5' leader uORFs [PMID:32938929], drives repeat-associated non-AUG (RAN) translation of C9orf72 GGGGCC expansions into toxic dipeptide-repeat proteins [PMID:34654821], and enables IRES-independent translation of the enterovirus genome when the eIF2-dependent pathway is inactivated [PMID:36689548]. Its reinitiation function at specific uORFs is mechanistically distinct from MCTS1-DENR, and eIF2D loss causes widespread gene deregulation beyond uORF control [PMID:39748120]. eIF2D is dispensable for HCV IRES-driven and Sindbis virus subgenomic mRNA translation [PMID:28240315, PMID:29487587]. Translation of eIF2D's own mRNA is downregulated during hyperosmotic stress through a uORF stop-codon-dependent mechanism [PMID:30419262].","teleology":[{"year":2017,"claim":"Establishing the domain architecture of eIF2D was needed to rationalize how a single factor could engage the ribosome like a canonical initiation factor yet carry an unusual module; the structure revealed an eIF1-like domain plus a SWIB/MDM2 fold.","evidence":"X-ray crystallography of the human eIF2D C-terminal domains at 1.4 A","pmids":["28736176"],"confidence":"High","gaps":["Full-length structure and the role of the N-terminal/winged helix regions not resolved","No ribosome-bound structure to show how the domains contact the 40S","Functional consequences of inter-domain interactions untested"]},{"year":2018,"claim":"It was unknown whether eIF2D acts physiologically after termination; deletion studies showed it (with MCT-1/DENR) recycles 40S subunits at stop codons and suppresses aberrant downstream reinitiation.","evidence":"Ribosome profiling of yeast deletion strains, 3' UTR reporters, in vitro translation","pmids":["30146315"],"confidence":"High","gaps":["Relative contribution of eIF2D vs the MCT-1/DENR heterodimer not quantified","Direct biochemical demonstration of 40S release by eIF2D alone lacking"]},{"year":2018,"claim":"To define the boundaries of eIF2D function in noncanonical viral translation, knockouts tested its requirement for IRES- and stress-driven viral synthesis; eIF2D proved dispensable for HCV IRES and Sindbis subgenomic mRNA translation.","evidence":"CRISPR/Cas9 and siRNA depletion in HAP1 cells with IRES-luciferase and viral protein synthesis assays","pmids":["28240315","29487587"],"confidence":"Medium","gaps":["Negative results do not exclude redundancy with other factors","Single-lab findings without orthogonal confirmation"]},{"year":2018,"claim":"How eIF2D's own expression is tuned under stress was unknown; reporter dissection revealed selective downregulation during hyperosmotic stress via a uORF stop-codon-dependent mechanism distinct from delayed reinitiation or stalling.","evidence":"Reporter mRNA assays and the FLERT technique with uORF mutational analysis","pmids":["30419262"],"confidence":"Medium","gaps":["Trans-acting factors mediating this autoregulation not identified","Physiological consequence of lowered eIF2D during stress not measured"]},{"year":2020,"claim":"Whether eIF2D contributes to stress-responsive gene expression was open; genetic and domain analyses placed eIF2D/DENR as critical for ATF4 translational induction during the integrated stress response, requiring its RNA-binding motif.","evidence":"Drosophila loss-of-function epistasis, RNA-binding motif mutagenesis, human cell ATF4 induction under ER stress","pmids":["32938929"],"confidence":"High","gaps":["Direct RNA target sequences bound by the RNA-binding motif not mapped","Step in the ATF4 5' leader reinitiation cycle that eIF2D acts on not pinpointed"]},{"year":2021,"claim":"The minor stop-codon recycling role of eIF2D was clarified by direct intermediate detection; 40S footprinting confirmed unrecycled 40S accumulation upon TMA64 loss but assigned the bulk of recycling to MCT-1/DENR.","evidence":"40S selective ribosome footprinting in yeast deletion strains","pmids":["34016977"],"confidence":"High","gaps":["Why eIF2D contributes little at canonical stop codons left unexplained until later structural reasoning","Substrate contexts where eIF2D dominates not defined here"]},{"year":2021,"claim":"It was unknown whether eIF2D participates in pathogenic noncanonical initiation; loss-of-function across species showed eIF2D promotes RAN translation of C9orf72 repeats, reducing dipeptide-repeat toxicity.","evidence":"C. elegans loss-of-function genetics, mammalian cell assays, lifespan readouts measuring poly-GA/poly-GP","pmids":["34654821"],"confidence":"High","gaps":["Mechanism by which eIF2D initiates at the repeat (codon/frame selection) not resolved","Whether this is direct or via its recycling activity unclear"]},{"year":2023,"claim":"The scope of eIF2D in viral noncanonical initiation was extended; depletion showed eIF2D with eIF2A is required for IRES-independent enterovirus genome translation when eIF2 is inactive, enabling recombination.","evidence":"Genetic depletion of eIF2A/eIF2D, viral replication/recombination assays, translation reporters","pmids":["36689548"],"confidence":"Medium","gaps":["Individual contribution of eIF2D vs eIF2A not separated","Single-lab finding with viral readout rather than direct biochemistry"]},{"year":2025,"claim":"The basis for eIF2D's mechanistic divergence from MCTS1-DENR was unresolved; TCP-seq and domain analysis showed eIF2D specializes in 40S recycling during intrinsic ribosome destabilization via its unique winged helix domain, which clashes with ABCE1 at canonical termination.","evidence":"TCP-seq selective translation complex profiling, eIF2D-deficient cells, domain structure-function analysis","pmids":["41335470"],"confidence":"High","gaps":["Proposed ABCE1 clash inferred rather than structurally demonstrated","Full set of IRD-prone substrates in vivo not enumerated"]},{"year":2025,"claim":"Whether eIF2D's reinitiation role overlaps with MCTS1-DENR was tested; cell-free assays and knockdown profiling distinguished eIF2D's uORF reinitiation activity and revealed widespread gene deregulation beyond uORF control.","evidence":"Cell-free reinitiation assay in HeLa lysates, ribosome profiling in knockdown cells, uORF reporters","pmids":["39748120"],"confidence":"Medium","gaps":["Direct mechanism linking eIF2D loss to non-uORF gene deregulation unknown","Single-lab in vitro reconstitution"]},{"year":null,"claim":"A unified structural and biochemical account of how eIF2D selects which post-termination/noncanonical initiation events to act on, and how its RNA-binding motif and winged helix domain coordinate recycling versus reinitiation in vivo, remains open.","evidence":"","pmids":[],"confidence":"High","gaps":["No ribosome-bound structure of eIF2D capturing recycling or reinitiation","RNA target specificity of the RNA-binding motif not defined","Rules dictating when eIF2D versus MCTS1-DENR is deployed not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[1,6,5]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[5]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[1,6,9]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[10]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,6,9]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5,10]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[5,4]}],"complexes":[],"partners":["DENR","MCTS1","EIF2A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P41214","full_name":"Eukaryotic translation initiation factor 2D","aliases":["Hepatocellular carcinoma-associated antigen 56","Ligatin"],"length_aa":584,"mass_kda":64.7,"function":"Translation initiation factor that is able to deliver tRNA to the P-site of the eukaryotic ribosome in a GTP-independent manner. The binding of Met-tRNA(I) occurs after the AUG codon finds its position in the P-site of 40S ribosomes, the situation that takes place during initiation complex formation on some specific RNAs. Its activity in tRNA binding with 40S subunits does not require the presence of the aminoacyl moiety. Possesses the unique ability to deliver non-Met (elongator) tRNAs into the P-site of the 40S subunit. In addition to its role in initiation, can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P41214/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EIF2D","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DNAJC18","stoichiometry":0.2},{"gene":"EIF3G","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/EIF2D","total_profiled":1310},"omim":[{"mim_id":"613709","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 2D; EIF2D","url":"https://www.omim.org/entry/613709"},{"mim_id":"151625","title":"LIGATIN; LGTN","url":"https://www.omim.org/entry/151625"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/EIF2D"},"hgnc":{"alias_symbol":["LGTN"],"prev_symbol":[]},"alphafold":{"accession":"P41214","domains":[{"cath_id":"3.10.400.20","chopping":"8-180","consensus_level":"high","plddt":87.5221,"start":8,"end":180},{"cath_id":"1.10.10","chopping":"262-355","consensus_level":"high","plddt":72.81,"start":262,"end":355},{"cath_id":"1.10.245.10","chopping":"381-474","consensus_level":"high","plddt":89.6138,"start":381,"end":474},{"cath_id":"3.30.780.10","chopping":"490-577","consensus_level":"high","plddt":89.195,"start":490,"end":577}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P41214","model_url":"https://alphafold.ebi.ac.uk/files/AF-P41214-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P41214-F1-predicted_aligned_error_v6.png","plddt_mean":76.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EIF2D","jax_strain_url":"https://www.jax.org/strain/search?query=EIF2D"},"sequence":{"accession":"P41214","fasta_url":"https://rest.uniprot.org/uniprotkb/P41214.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P41214/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P41214"}},"corpus_meta":[{"pmid":"32938929","id":"PMC_32938929","title":"Translational induction of ATF4 during integrated stress response requires noncanonical initiation factors eIF2D and DENR.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32938929","citation_count":73,"is_preprint":false},{"pmid":"30146315","id":"PMC_30146315","title":"Tma64/eIF2D, Tma20/MCT-1, and Tma22/DENR Recycle Post-termination 40S Subunits In Vivo.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30146315","citation_count":67,"is_preprint":false},{"pmid":"34654821","id":"PMC_34654821","title":"A C. elegans model of C9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34654821","citation_count":41,"is_preprint":false},{"pmid":"34016977","id":"PMC_34016977","title":"40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34016977","citation_count":32,"is_preprint":false},{"pmid":"28240315","id":"PMC_28240315","title":"Translation of Sindbis Subgenomic mRNA is Independent of eIF2, eIF2A and eIF2D.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28240315","citation_count":28,"is_preprint":false},{"pmid":"29487587","id":"PMC_29487587","title":"The Initiation Factors eIF2, eIF2A, eIF2D, eIF4A, and eIF4G Are Not Involved in Translation Driven by Hepatitis C Virus IRES in Human Cells.","date":"2018","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29487587","citation_count":27,"is_preprint":false},{"pmid":"32487605","id":"PMC_32487605","title":"New Pancreatic Cancer Biomarkers eIF1, eIF2D, eIF3C and eIF6 Play a Major Role in Translational Control in Ductal Adenocarcinoma.","date":"2020","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/32487605","citation_count":26,"is_preprint":false},{"pmid":"28736176","id":"PMC_28736176","title":"Crystal Structure of the C-terminal Domain of Human eIF2D and Its Implications on Eukaryotic Translation Initiation.","date":"2017","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/28736176","citation_count":14,"is_preprint":false},{"pmid":"30815525","id":"PMC_30815525","title":"Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.","date":"2019","source":"Data in brief","url":"https://pubmed.ncbi.nlm.nih.gov/30815525","citation_count":13,"is_preprint":false},{"pmid":"30419262","id":"PMC_30419262","title":"A novel uORF-based regulatory mechanism controls translation of the human MDM2 and eIF2D mRNAs during stress.","date":"2018","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/30419262","citation_count":13,"is_preprint":false},{"pmid":"38433101","id":"PMC_38433101","title":"To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes.","date":"2024","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/38433101","citation_count":10,"is_preprint":false},{"pmid":"36689548","id":"PMC_36689548","title":"The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D.","date":"2023","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/36689548","citation_count":10,"is_preprint":false},{"pmid":"31078689","id":"PMC_31078689","title":"Time dependent expression of the blood biomarkers EIF2D and TOX in patients with schizophrenia.","date":"2019","source":"Brain, behavior, and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/31078689","citation_count":7,"is_preprint":false},{"pmid":"39748120","id":"PMC_39748120","title":"MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays.","date":"2025","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/39748120","citation_count":4,"is_preprint":false},{"pmid":"41335470","id":"PMC_41335470","title":"eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41335470","citation_count":0,"is_preprint":false},{"pmid":"41354083","id":"PMC_41354083","title":"In Search of Novel Diagnostic Biomarkers for Psychoneurological and Neurodegenerative Diseases: Translation Factors DENR and eIF2D.","date":"2025","source":"Biochemistry. Biokhimiia","url":"https://pubmed.ncbi.nlm.nih.gov/41354083","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9177,"output_tokens":2682,"usd":0.033881,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9912,"output_tokens":3923,"usd":0.073817,"stage2_stop_reason":"end_turn"},"total_usd":0.107698,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of the C-terminal domains of human eIF2D determined at 1.4-Å resolution, revealing one domain with a fold similar to eIF1 (important for scanning and initiation codon selection) and a second domain with a SWIB/MDM2 fold not previously observed in translation initiation factors, with atomic details of inter-domain interactions.\",\n      \"method\": \"X-ray crystallography\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure at 1.4-Å resolution with domain-fold assignments; single study but high-resolution structural data\",\n      \"pmids\": [\"28736176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Yeast Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S ribosomal subunit recycling factors in vivo at stop codons; deletion strains showed 80S ribosomes queued behind stop codons, unrecycled ribosomes reinitiated at 3' UTR AUG codons, and in vitro translation experiments confirmed increased reinitiation at uORFs in their absence.\",\n      \"method\": \"Ribosome profiling of deletion strains, 3' UTR reporter analysis, in vitro translation assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — ribosome profiling combined with in vitro translation and reporter assays, replicated across multiple deletion strains and methods\",\n      \"pmids\": [\"30146315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"eIF2D and eIF2A are NOT required for translation of Sindbis virus subgenomic mRNA under conditions of eIF2α phosphorylation; CRISPR/Cas9 knockout of eIF2D in HAP1 cells showed comparable viral protein synthesis to wild-type cells.\",\n      \"method\": \"CRISPR/Cas9 knockout cell lines, viral infection and protein synthesis assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined functional readout, but single lab; negative finding confirmed by siRNA knockdown as well\",\n      \"pmids\": [\"28240315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"eIF2D and eIF2A are NOT required for HCV IRES-driven translation in human cells; HAP1 cells depleted for eIF2D (individually or combined with eIF2A) synthesized luciferase from HCV IRES-bearing mRNA even when eIF2α was phosphorylated.\",\n      \"method\": \"HAP1 knockout cell lines, IRES-reporter luciferase assay\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with functional reporter assay, single lab; negative result confirmed across multiple conditions\",\n      \"pmids\": [\"29487587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Translation of the eIF2D mRNA itself is selectively downregulated during hyperosmotic stress via a novel uORF-based regulatory mechanism dependent on events at the uORF stop codon or immediately downstream, distinct from delayed reinitiation, altered AUG recognition, ribosome stalling, or mRNA destabilization.\",\n      \"method\": \"Reporter mRNA assays, fleeting mRNA transfection (FLERT) technique with mutational analysis of uORF elements\",\n      \"journal\": \"Biochimie\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple reporter constructs and FLERT technique in single lab with mechanistic dissection\",\n      \"pmids\": [\"30419262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"eIF2D and DENR are critical mediators of ATF4 translational induction during the integrated stress response; loss of eIF2D and DENR in Drosophila phenocopies ATF4 mutants, and eIF2D requires its RNA-binding motif for regulation of 5' leader-mediated ATF4 translation. eIF2D/DENR-deficient human cells show impaired ATF4 protein induction in response to ER stress.\",\n      \"method\": \"Drosophila genetic loss-of-function, domain mutational analysis (RNA-binding motif), human cell knockdown with ATF4 protein induction assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis in Drosophila, domain mutagenesis, and human cell validation across multiple stress conditions\",\n      \"pmids\": [\"32938929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"40S ribosome footprinting directly demonstrated that deletion of TMA64 (eIF2D) leads to accumulation of unrecycled 40S subunits at stop codons; however, the Tma20/Tma22 (MCT-1/DENR) heterodimer was responsible for the majority of 40S recycling events, while Tma64 played a minor role.\",\n      \"method\": \"40S ribosome footprinting (selective ribosome profiling) in deletion strains\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct footprinting of recycling intermediates with multiple deletion strains; replicated and extended earlier findings\",\n      \"pmids\": [\"34016977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"eIF2D (eif-2D) promotes repeat-associated non-AUG (RAN) translation of C9orf72 GGGGCC repeat expansions; loss-of-function mutations in eif-2D in C. elegans reduced poly-GA and poly-GP dipeptide repeat protein levels and increased lifespan in disease models. In vitro studies in mammalian cells yielded similar results, establishing a conserved role for eIF2D in DPR expression.\",\n      \"method\": \"C. elegans loss-of-function genetics, mammalian cell in vitro studies, lifespan assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function in C. elegans plus mammalian cell validation, multiple DPR species measured across two independent model systems\",\n      \"pmids\": [\"34654821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"eIF2D (together with eIF2A) is required for IRES-independent translation of the enterovirus genome under conditions in which the eIF2-dependent mechanism is inactive; this noncanonical mechanism supports sufficient translation of nonstructural regions to permit genome recombination.\",\n      \"method\": \"Genetic depletion of eIF2A/eIF2D, viral replication and recombination assays, translation reporters\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional depletion experiments with viral replication readout, single lab, two factors tested together making individual contributions unclear\",\n      \"pmids\": [\"36689548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"eIF2D promotes 40S ribosomal subunit recycling specifically during intrinsic ribosome destabilization (IRD), a process occurring when ribosomes translate proteins with consecutive acidic amino acids at their N-terminus. Selective translation complex profiling (TCP-seq) showed eIF2D preferentially associates with IRD-prone regions. The winged helix domain unique to eIF2D (absent in MCTS1-DENR) enhances binding to 40S subunits but likely clashes with ABCE1 during stop-codon-associated recycling, explaining mechanistic divergence from MCTS1-DENR.\",\n      \"method\": \"TCP-seq (selective translation complex profiling), eIF2D-deficient cells, domain structure-function analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — TCP-seq profiling with domain mutational analysis and functional readout in KO cells; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"41335470\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Knockdown of eIF2D causes widespread gene deregulation unrelated to uORF translation, distinguishing its function from MCTS1-DENR-dependent re-initiation regulation; in cell-free re-initiation assays using HeLa lysates, eIF2D's role in re-initiation at specific uORFs was found to be distinct from that of MCTS1-DENR.\",\n      \"method\": \"Cell-free re-initiation assay (HeLa lysates), ribosome profiling in knockdown cells, uORF reporters\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro reconstitution assay combined with ribosome profiling and knockdown, single lab\",\n      \"pmids\": [\"39748120\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"eIF2D is a noncanonical translation initiation factor whose C-terminal region contains an eIF1-like domain and a SWIB/MDM2 domain; it promotes 40S ribosomal subunit recycling (particularly during intrinsic ribosome destabilization via its unique winged helix domain), mediates translation reinitiation at upstream ORFs, drives ATF4 translational induction during integrated stress response through its RNA-binding motif, supports RAN translation of C9orf72 repeat expansions, and enables IRES-independent translation of enteroviral genomes — while being dispensable for HCV IRES-driven and Sindbis virus subgenomic mRNA translation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"eIF2D is a noncanonical translation factor that acts at the interface of 40S ribosomal subunit recycling and reinitiation, governing the post-termination and noncanonical-initiation fates of ribosomes [#1, #6]. Structurally it pairs an eIF1-like domain (linked to scanning and initiation codon selection) with a SWIB/MDM2 fold not previously seen among initiation factors, providing the architecture for its dual roles [#0]. In yeast and in 40S footprinting assays, eIF2D (Tma64) recycles 40S subunits stranded at stop codons, preventing aberrant reinitiation at downstream AUG and 3' UTR codons, although the MCT-1/DENR heterodimer carries the bulk of canonical stop-codon recycling and eIF2D plays a comparatively minor role there [#1, #6]. eIF2D's mechanistic specialization is its winged helix domain, absent from MCTS1-DENR, which enhances 40S binding and directs eIF2D toward recycling during intrinsic ribosome destabilization at nascent N-terminal acidic stretches, a context where it would clash with ABCE1 in conventional termination-coupled recycling [#9]. Through these activities eIF2D supports specialized translation programs: it mediates ATF4 translational induction during the integrated stress response via its RNA-binding motif and 5' leader uORFs [#5], drives repeat-associated non-AUG (RAN) translation of C9orf72 GGGGCC expansions into toxic dipeptide-repeat proteins [#7], and enables IRES-independent translation of the enterovirus genome when the eIF2-dependent pathway is inactivated [#8]. Its reinitiation function at specific uORFs is mechanistically distinct from MCTS1-DENR, and eIF2D loss causes widespread gene deregulation beyond uORF control [#10]. eIF2D is dispensable for HCV IRES-driven and Sindbis virus subgenomic mRNA translation [#2, #3]. Translation of eIF2D's own mRNA is downregulated during hyperosmotic stress through a uORF stop-codon-dependent mechanism [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing the domain architecture of eIF2D was needed to rationalize how a single factor could engage the ribosome like a canonical initiation factor yet carry an unusual module; the structure revealed an eIF1-like domain plus a SWIB/MDM2 fold.\",\n      \"evidence\": \"X-ray crystallography of the human eIF2D C-terminal domains at 1.4 A\",\n      \"pmids\": [\"28736176\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full-length structure and the role of the N-terminal/winged helix regions not resolved\",\n        \"No ribosome-bound structure to show how the domains contact the 40S\",\n        \"Functional consequences of inter-domain interactions untested\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"It was unknown whether eIF2D acts physiologically after termination; deletion studies showed it (with MCT-1/DENR) recycles 40S subunits at stop codons and suppresses aberrant downstream reinitiation.\",\n      \"evidence\": \"Ribosome profiling of yeast deletion strains, 3' UTR reporters, in vitro translation\",\n      \"pmids\": [\"30146315\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Relative contribution of eIF2D vs the MCT-1/DENR heterodimer not quantified\",\n        \"Direct biochemical demonstration of 40S release by eIF2D alone lacking\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"To define the boundaries of eIF2D function in noncanonical viral translation, knockouts tested its requirement for IRES- and stress-driven viral synthesis; eIF2D proved dispensable for HCV IRES and Sindbis subgenomic mRNA translation.\",\n      \"evidence\": \"CRISPR/Cas9 and siRNA depletion in HAP1 cells with IRES-luciferase and viral protein synthesis assays\",\n      \"pmids\": [\"28240315\", \"29487587\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Negative results do not exclude redundancy with other factors\",\n        \"Single-lab findings without orthogonal confirmation\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"How eIF2D's own expression is tuned under stress was unknown; reporter dissection revealed selective downregulation during hyperosmotic stress via a uORF stop-codon-dependent mechanism distinct from delayed reinitiation or stalling.\",\n      \"evidence\": \"Reporter mRNA assays and the FLERT technique with uORF mutational analysis\",\n      \"pmids\": [\"30419262\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Trans-acting factors mediating this autoregulation not identified\",\n        \"Physiological consequence of lowered eIF2D during stress not measured\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether eIF2D contributes to stress-responsive gene expression was open; genetic and domain analyses placed eIF2D/DENR as critical for ATF4 translational induction during the integrated stress response, requiring its RNA-binding motif.\",\n      \"evidence\": \"Drosophila loss-of-function epistasis, RNA-binding motif mutagenesis, human cell ATF4 induction under ER stress\",\n      \"pmids\": [\"32938929\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct RNA target sequences bound by the RNA-binding motif not mapped\",\n        \"Step in the ATF4 5' leader reinitiation cycle that eIF2D acts on not pinpointed\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The minor stop-codon recycling role of eIF2D was clarified by direct intermediate detection; 40S footprinting confirmed unrecycled 40S accumulation upon TMA64 loss but assigned the bulk of recycling to MCT-1/DENR.\",\n      \"evidence\": \"40S selective ribosome footprinting in yeast deletion strains\",\n      \"pmids\": [\"34016977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Why eIF2D contributes little at canonical stop codons left unexplained until later structural reasoning\",\n        \"Substrate contexts where eIF2D dominates not defined here\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"It was unknown whether eIF2D participates in pathogenic noncanonical initiation; loss-of-function across species showed eIF2D promotes RAN translation of C9orf72 repeats, reducing dipeptide-repeat toxicity.\",\n      \"evidence\": \"C. elegans loss-of-function genetics, mammalian cell assays, lifespan readouts measuring poly-GA/poly-GP\",\n      \"pmids\": [\"34654821\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism by which eIF2D initiates at the repeat (codon/frame selection) not resolved\",\n        \"Whether this is direct or via its recycling activity unclear\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The scope of eIF2D in viral noncanonical initiation was extended; depletion showed eIF2D with eIF2A is required for IRES-independent enterovirus genome translation when eIF2 is inactive, enabling recombination.\",\n      \"evidence\": \"Genetic depletion of eIF2A/eIF2D, viral replication/recombination assays, translation reporters\",\n      \"pmids\": [\"36689548\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Individual contribution of eIF2D vs eIF2A not separated\",\n        \"Single-lab finding with viral readout rather than direct biochemistry\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The basis for eIF2D's mechanistic divergence from MCTS1-DENR was unresolved; TCP-seq and domain analysis showed eIF2D specializes in 40S recycling during intrinsic ribosome destabilization via its unique winged helix domain, which clashes with ABCE1 at canonical termination.\",\n      \"evidence\": \"TCP-seq selective translation complex profiling, eIF2D-deficient cells, domain structure-function analysis\",\n      \"pmids\": [\"41335470\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Proposed ABCE1 clash inferred rather than structurally demonstrated\",\n        \"Full set of IRD-prone substrates in vivo not enumerated\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether eIF2D's reinitiation role overlaps with MCTS1-DENR was tested; cell-free assays and knockdown profiling distinguished eIF2D's uORF reinitiation activity and revealed widespread gene deregulation beyond uORF control.\",\n      \"evidence\": \"Cell-free reinitiation assay in HeLa lysates, ribosome profiling in knockdown cells, uORF reporters\",\n      \"pmids\": [\"39748120\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct mechanism linking eIF2D loss to non-uORF gene deregulation unknown\",\n        \"Single-lab in vitro reconstitution\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A unified structural and biochemical account of how eIF2D selects which post-termination/noncanonical initiation events to act on, and how its RNA-binding motif and winged helix domain coordinate recycling versus reinitiation in vivo, remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No ribosome-bound structure of eIF2D capturing recycling or reinitiation\",\n        \"RNA target specificity of the RNA-binding motif not defined\",\n        \"Rules dictating when eIF2D versus MCTS1-DENR is deployed not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [1, 6, 5]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [1, 6, 9]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72613\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 6, 9]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5, 10]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [5, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"DENR\",\n      \"MCTS1\",\n      \"EIF2A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}