- EMDB-13111: Cryo-EM structure of the 1 hpf zebrafish embryo 80S ribosome -
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基本情報
登録情報
データベース: EMDB / ID: EMD-13111
タイトル
Cryo-EM structure of the 1 hpf zebrafish embryo 80S ribosome
マップデータ
試料
複合体: 80S ribosome from 1 hpf zebrafish embryos
RNA: x 4種
タンパク質・ペプチド: x 78種
リガンド: x 2種
機能・相同性
機能・相同性情報
Hypusine synthesis from eIF5A-lysine / Platelet degranulation / optokinetic behavior / regulation of mRNA cis splicing, via spliceosome / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...Hypusine synthesis from eIF5A-lysine / Platelet degranulation / optokinetic behavior / regulation of mRNA cis splicing, via spliceosome / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RMTs methylate histone arginines / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / GLI3 is processed to GLI3R by the proteasome / TNFR1-mediated ceramide production / Hedgehog 'on' state / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Negative regulation of MET activity / Assembly of the pre-replicative complex / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / Protein methylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Regulation of signaling by CBL / Endosomal Sorting Complex Required For Transport (ESCRT) / Protein hydroxylation / KEAP1-NFE2L2 pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of innate immune responses to cytosolic DNA / Deactivation of the beta-catenin transactivating complex / CDK-mediated phosphorylation and removal of Cdc6 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of RUNX3 expression and activity / mTORC1-mediated signalling / Regulation of FZD by ubiquitination / brain segmentation / p75NTR recruits signalling complexes / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Interleukin-1 signaling / nucleate erythrocyte maturation / ABC-family proteins mediated transport / Antigen processing: Ubiquitination & Proteasome degradation / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / convergent extension involved in gastrulation / Ovarian tumor domain proteases / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Ub-specific processing proteases / Neddylation / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / The role of GTSE1 in G2/M progression after G2 checkpoint / convergent extension involved in axis elongation / Neutrophil degranulation / primitive hemopoiesis / embryonic retina morphogenesis in camera-type eye / anatomical structure development / death domain binding / positive regulation of translational termination 類似検索 - 分子機能
DAP1/DAPL1 / Death-associated protein / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / PA2G4 family / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold ...DAP1/DAPL1 / Death-associated protein / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / PA2G4 family / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Peptidase M24 / Ubiquitin-like protein FUBI / Elongation Factor G, domain II / Elongation Factor G, domain III / Metallopeptidase family M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Creatinase/aminopeptidase-like / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / EF-G domain III/V-like / : / Ribosomal protein S26e signature. / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e 類似検索 - ドメイン・相同性
60S ribosomal protein L41 / Large ribosomal subunit protein eL24 / 60S ribosomal protein L37a / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Zgc:103482 / 40S ribosomal protein S24 / 60S ribosomal protein L28 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL23 ...60S ribosomal protein L41 / Large ribosomal subunit protein eL24 / 60S ribosomal protein L37a / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Zgc:103482 / 40S ribosomal protein S24 / 60S ribosomal protein L28 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / 40S ribosomal protein S16 / Large ribosomal subunit protein uL13 / 60S ribosomal protein L32 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S27 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein eS4 / Ribosomal protein L18 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL33 / 40S ribosomal protein S6 / Ribosomal protein L15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL39 / Ribosomal protein L5 / Large ribosomal subunit protein uL5 / Ribosomal protein L37 / 60S ribosomal protein L21 / Small ribosomal subunit protein uS5 / Eukaryotic translation initiation factor 5A / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL15 / Eukaryotic translation elongation factor 2 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein uS4 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S19 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L7a / 40S ribosomal protein S30 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Ribosomal protein S10 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL16 / DNA-(apurinic or apyrimidinic site) lyase / Ribosomal protein L4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS2 / Novel protein similar to human proliferation-associated 2G4 protein (PA2G4) / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL13 / Death-associated protein-like 1 homolog 類似検索 - 構成要素
ジャーナル: Nature / 年: 2023 タイトル: A molecular network of conserved factors keeps ribosomes dormant in the egg. 著者: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne ...著者: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne Kandolf / Tzi-Yang Lin / Karl Mechtler / Anton Meinhart / David Haselbach / Andrea Pauli / 要旨: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron ...Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.