+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11456 | ||||||||||||
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タイトル | EDF1-ribosome complex | ||||||||||||
マップデータ | Map of EDF1 bound to 80S ribosomes, (local resolution filtered). | ||||||||||||
試料 |
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キーワード | translation (翻訳 (生物学)) / frameshifting (フレームシフト突然変異) / collision (衝突) / RIBOSOME (リボソーム) | ||||||||||||
機能・相同性 | 機能・相同性情報 endothelial cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation ...endothelial cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / negative regulation of phagocytosis / NF-kappaB complex / rRNA modification in the nucleus and cytosol / transcription regulator inhibitor activity / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / 顔料 / protein kinase A binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / erythrocyte development / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of transcription by RNA polymerase I / fibroblast growth factor binding / positive regulation of activated T cell proliferation / regulation of cell division / ヒドロキシル化 / MTOR / iron-sulfur cluster binding / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / TFIID-class transcription factor complex binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / translation regulator activity / Viral mRNA Translation / regulation of lipid metabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / photoreceptor outer segment / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / gastrulation / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 小胞体 / regulation of translational fidelity / spindle assembly / MDM2/MDM4 family protein binding / positive regulation of DNA binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / rescue of stalled ribosome / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of cell cycle / positive regulation of phagocytosis / translation initiation factor binding / stress granule assembly / negative regulation of peptidyl-serine phosphorylation / maturation of SSU-rRNA 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | ||||||||||||
データ登録者 | Best KM / Denk T | ||||||||||||
資金援助 | ドイツ, 米国, 3件
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引用 | ジャーナル: Elife / 年: 2020 タイトル: EDF1 coordinates cellular responses to ribosome collisions. 著者: Niladri K Sinha / Alban Ordureau / Katharina Best / James A Saba / Boris Zinshteyn / Elayanambi Sundaramoorthy / Amit Fulzele / Danielle M Garshott / Timo Denk / Matthias Thoms / Joao A Paulo ...著者: Niladri K Sinha / Alban Ordureau / Katharina Best / James A Saba / Boris Zinshteyn / Elayanambi Sundaramoorthy / Amit Fulzele / Danielle M Garshott / Timo Denk / Matthias Thoms / Joao A Paulo / J Wade Harper / Eric J Bennett / Roland Beckmann / Rachel Green / 要旨: Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation ...Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation. | ||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_11456.map.gz | 139.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11456-v30.xml emd-11456.xml | 53.1 KB 53.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11456_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_11456.png | 208.4 KB | ||
マスクデータ | emd_11456_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-11456.cif.gz | 10.9 KB | ||
その他 | emd_11456_additional.map.gz emd_11456_half_map_1.map.gz emd_11456_half_map_2.map.gz | 17.8 MB 192.9 MB 192.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11456 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_11456.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Map of EDF1 bound to 80S ribosomes, (local resolution filtered). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | emd_11456_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Post processed map, bFactor -30
ファイル | emd_11456_additional.map | ||||||||||||
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注釈 | Post processed map, bFactor -30 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2 of the 3D refinement
ファイル | emd_11456_half_map_1.map | ||||||||||||
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注釈 | Half map 2 of the 3D refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 of the 3D refinement
ファイル | emd_11456_half_map_2.map | ||||||||||||
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注釈 | Half map 1 of the 3D refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : EDF1-ribosome complex
+超分子 #1: EDF1-ribosome complex
+分子 #1: 18S rRNA
+分子 #35: E-site tRNA
+分子 #2: 40S ribosomal protein SA
+分子 #3: 40S ribosomal protein S3a
+分子 #4: 40S ribosomal protein S3
+分子 #5: 40S ribosomal protein S4, X isoform
+分子 #6: 40S ribosomal protein S5
+分子 #7: 40S ribosomal protein S7
+分子 #8: 40S ribosomal protein S8
+分子 #9: 40S ribosomal protein S10
+分子 #10: 40S ribosomal protein S11
+分子 #11: 40S ribosomal protein S15
+分子 #12: 40S ribosomal protein S16
+分子 #13: 40S ribosomal protein S17
+分子 #14: 40S ribosomal protein S18
+分子 #15: 40S ribosomal protein S19
+分子 #16: 40S ribosomal protein S20
+分子 #17: 40S ribosomal protein S21
+分子 #18: 40S ribosomal protein S23
+分子 #19: 40S ribosomal protein S26
+分子 #20: 40S ribosomal protein S28
+分子 #21: 40S ribosomal protein S29
+分子 #22: Receptor of activated protein C kinase 1
+分子 #23: 40S ribosomal protein S2
+分子 #24: 40S ribosomal protein S6
+分子 #25: 40S ribosomal protein S9
+分子 #26: 40S ribosomal protein S12
+分子 #27: 40S ribosomal protein S13
+分子 #28: 40S ribosomal protein S14
+分子 #29: 40S ribosomal protein S15a
+分子 #30: 40S ribosomal protein S24
+分子 #31: 40S ribosomal protein S25
+分子 #32: 40S ribosomal protein S27
+分子 #33: 40S ribosomal protein S30
+分子 #34: Ubiquitin-40S ribosomal protein S27a
+分子 #36: Cell growth-regulating nucleolar protein
+分子 #37: Endothelial differentiation-related factor 1
+分子 #38: MAGNESIUM ION
+分子 #39: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 28.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |