+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10377 | |||||||||
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タイトル | Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. | |||||||||
マップデータ | Yeast 80S ribosome stalled on CGA-CCG inhibitory di-codon | |||||||||
試料 |
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キーワード | stalling dicodon codon pair / TRANSLATION | |||||||||
機能・相同性 | 機能・相同性情報 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / regulation of translational fidelity / protein-RNA complex assembly / Ub-specific processing proteases / ribosomal small subunit export from nucleus / translation regulator activity / ribosomal subunit export from nucleus / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | |||||||||
データ登録者 | Tesina P / Buschauer R | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: EMBO J / 年: 2020 タイトル: Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. 著者: Petr Tesina / Laura N Lessen / Robert Buschauer / Jingdong Cheng / Colin Chih-Chien Wu / Otto Berninghausen / Allen R Buskirk / Thomas Becker / Roland Beckmann / Rachel Green / 要旨: Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still ...Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes. | |||||||||
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_10377.map.gz | 143.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10377-v30.xml emd-10377.xml | 93.9 KB 93.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10377_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_10377.png | 200.5 KB | ||
Filedesc metadata | emd-10377.cif.gz | 17.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10377 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10377 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10377_validation.pdf.gz | 288.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10377_full_validation.pdf.gz | 287.4 KB | 表示 | |
XML形式データ | emd_10377_validation.xml.gz | 13.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10377 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10377 | 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_10377.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 | Yeast 80S ribosome stalled on CGA-CCG inhibitory di-codon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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
-試料の構成要素
+全体 : yeast 80S ribosome stalled on CGA-CCG inhibitory codon combination
+超分子 #1: yeast 80S ribosome stalled on CGA-CCG inhibitory codon combination
+分子 #1: 18S rRNA
+分子 #34: 5S rRNA
+分子 #35: 5.8S rRNA
+分子 #77: 25S rRNA
+分子 #78: mRNA
+分子 #79: ICG tRNA Arg (P/P)
+分子 #80: tRNA (E/E)
+分子 #2: 40S ribosomal protein S1-A
+分子 #3: 40S ribosomal protein S15
+分子 #4: 40S ribosomal protein S2
+分子 #5: 40S ribosomal protein S3
+分子 #6: 40S ribosomal protein S4-A
+分子 #7: Rps5p
+分子 #8: 40S ribosomal protein S6-A
+分子 #9: 40S ribosomal protein S7-A
+分子 #10: 40S ribosomal protein S8-A
+分子 #11: 40S ribosomal protein S9-A
+分子 #12: 40S ribosomal protein S10-A
+分子 #13: 40S ribosomal protein S11-A
+分子 #14: 40S ribosomal protein S12
+分子 #15: 40S ribosomal protein S13
+分子 #16: 40S ribosomal protein S14-B
+分子 #17: 40S ribosomal protein S16-A
+分子 #18: 40S ribosomal protein S17-A
+分子 #19: 40S ribosomal protein S18-A
+分子 #20: 40S ribosomal protein S19-A
+分子 #21: 40S ribosomal protein S20
+分子 #22: 40S ribosomal protein S21-A
+分子 #23: 40S ribosomal protein S22-A
+分子 #24: 40S ribosomal protein S23-A
+分子 #25: 40S ribosomal protein S24-A
+分子 #26: 40S ribosomal protein S25-A
+分子 #27: 40S ribosomal protein S26-B
+分子 #28: 40S ribosomal protein S27-A
+分子 #29: 40S ribosomal protein S29-A
+分子 #30: 40S ribosomal protein S30-A
+分子 #31: Ubiquitin-40S ribosomal protein S31
+分子 #32: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #33: 40S ribosomal protein S28-A
+分子 #36: 60S ribosomal protein L2-A
+分子 #37: 60S ribosomal protein L3
+分子 #38: 60S ribosomal protein L4-A
+分子 #39: 60S ribosomal protein L5
+分子 #40: 60S ribosomal protein L6-B
+分子 #41: 60S ribosomal protein L7-A
+分子 #42: 60S ribosomal protein L8-A
+分子 #43: 60S ribosomal protein L9-A
+分子 #44: 60S ribosomal protein L10
+分子 #45: 60S ribosomal protein L11-B
+分子 #46: 60S ribosomal protein L13-A
+分子 #47: 60S ribosomal protein L14-A
+分子 #48: 60S ribosomal protein L15-A
+分子 #49: 60S ribosomal protein L16-A
+分子 #50: 60S ribosomal protein L17-A
+分子 #51: 60S ribosomal protein L18-A
+分子 #52: 60S ribosomal protein L19-A
+分子 #53: 60S ribosomal protein L20-A
+分子 #54: 60S ribosomal protein L21-A
+分子 #55: 60S ribosomal protein L22-A
+分子 #56: 60S ribosomal protein L23-A
+分子 #57: 60S ribosomal protein L24-A
+分子 #58: 60S ribosomal protein L25
+分子 #59: 60S ribosomal protein L26-A
+分子 #60: 60S ribosomal protein L27-A
+分子 #61: 60S ribosomal protein L28
+分子 #62: 60S ribosomal protein L29
+分子 #63: 60S ribosomal protein L30
+分子 #64: 60S ribosomal protein L31-A
+分子 #65: 60S ribosomal protein L32
+分子 #66: 60S ribosomal protein L33-A
+分子 #67: 60S ribosomal protein L34-A
+分子 #68: 60S ribosomal protein L35-A
+分子 #69: 60S ribosomal protein L36-A
+分子 #70: 60S ribosomal protein L37-A
+分子 #71: 60S ribosomal protein L38
+分子 #72: 60S ribosomal protein L39
+分子 #73: Ubiquitin-60S ribosomal protein L40
+分子 #74: 60S ribosomal protein L41-A
+分子 #75: 60S ribosomal protein L42-A
+分子 #76: 60S ribosomal protein L43-A
+分子 #81: nascent chain
+分子 #82: 40S ribosomal protein S0-A
+分子 #83: MAGNESIUM ION
+分子 #84: 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: 7.2 |
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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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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 2.5 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |