+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11456 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||
キーワード | translation / frameshifting / collision / RIBOSOME | ||||||||||||
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 / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway ...endothelial cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / transcription regulator inhibitor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / oxidized purine DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of DNA binding / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of transcription by RNA polymerase I / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / iron-sulfur cluster binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / Protein hydroxylation / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / 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 / cysteine-type endopeptidase activator activity involved in apoptotic process / TFIID-class transcription factor complex binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / regulation of lipid metabolic process / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / photoreceptor outer segment / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / translation regulator activity / signaling adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of phagocytosis / negative regulation of smoothened signaling pathway / stress granule assembly / Mitotic Prometaphase / laminin binding / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation 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
| ||||||||||||
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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | |
---|---|---|---|---|
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 |
-検証レポート
文書・要旨 | emd_11456_validation.pdf.gz | 959 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_11456_full_validation.pdf.gz | 958.6 KB | 表示 | |
XML形式データ | emd_11456_validation.xml.gz | 21.9 KB | 表示 | |
CIF形式データ | emd_11456_validation.cif.gz | 29 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11456 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11456 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Map of EDF1 bound to 80S ribosomes, (local resolution filtered). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-マスク #1
ファイル | emd_11456_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Post processed map, bFactor -30 | ||||||||||||
投影像・断面図 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half map 2 of the 3D refinement | ||||||||||||
投影像・断面図 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half map 1 of the 3D refinement | ||||||||||||
投影像・断面図 |
| ||||||||||||
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 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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 |
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 FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |