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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-0953 | |||||||||
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タイトル | Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) | |||||||||
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![]() | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / RIBOSOME | |||||||||
機能・相同性 | ![]() regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex ...regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / box C/D sno(s)RNA binding / regulation of rRNA processing / septum digestion after cytokinesis / histone H2AQ104 methyltransferase activity / tRNA re-export from nucleus / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / SUMOylation of RNA binding proteins / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / 90S preribosome assembly / rRNA methylation / mTORC1-mediated signalling / Protein hydroxylation / U4 snRNP / poly(U) RNA binding / U3 snoRNA 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 / precatalytic spliceosome / Ribosomal scanning and start codon recognition / snoRNA binding / preribosome, small subunit precursor / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / 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) / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / nuclear periphery / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / spliceosomal complex / translational initiation / small-subunit processome / enzyme activator activity / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing / peroxisome / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.9 Å | |||||||||
![]() | Du Y / Ye K | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states. 著者: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye / ![]() 要旨: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by ...The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 17.3 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 98.9 KB 98.9 KB | 表示 表示 | ![]() |
画像 | ![]() | 66.6 KB | ||
Filedesc metadata | ![]() | 26.7 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 411 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 410.5 KB | 表示 | |
XML形式データ | ![]() | 7.5 KB | 表示 | |
CIF形式データ | ![]() | 8.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6lqtMC ![]() 0949C ![]() 0950C ![]() 0951C ![]() 0952C ![]() 0954C ![]() 0955C ![]() 6lqpC ![]() 6lqqC ![]() 6lqrC ![]() 6lqsC ![]() 6lquC ![]() 6lqvC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.334 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
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試料の構成要素
+全体 : 90S pre-ribosome (Dhr1-depleted, state E)
+超分子 #1: 90S pre-ribosome (Dhr1-depleted, state E)
+分子 #1: U3 snoRNA
+分子 #2: 5' ETS
+分子 #3: 18S pre-rRNA
+分子 #4: 40S ribosomal protein S1-A
+分子 #5: 40S ribosomal protein S4-A
+分子 #6: 40S ribosomal protein S5
+分子 #7: 40S ribosomal protein S6-A
+分子 #8: 40S ribosomal protein S7-A
+分子 #9: 40S ribosomal protein S8-A
+分子 #10: 40S ribosomal protein S9-A
+分子 #11: 40S ribosomal protein S11-A
+分子 #12: 40S ribosomal protein S13
+分子 #13: 40S ribosomal protein S14-A
+分子 #14: 40S ribosomal protein S16-A
+分子 #15: 40S ribosomal protein S22-B
+分子 #16: 40S ribosomal protein S23-A
+分子 #17: 40S ribosomal protein S24-A
+分子 #18: 40S ribosomal protein S27-A
+分子 #19: 40S ribosomal protein S28-A
+分子 #20: rRNA 2'-O-methyltransferase fibrillarin
+分子 #21: Nucleolar protein 56
+分子 #22: Nucleolar protein 58
+分子 #23: Ribosomal RNA-processing protein 9
+分子 #24: 13 kDa ribonucleoprotein-associated protein
+分子 #25: U3 small nucleolar RNA-associated protein 4
+分子 #26: U3 small nucleolar RNA-associated protein 5
+分子 #27: U3 small nucleolar RNA-associated protein 9
+分子 #28: U3 small nucleolar RNA-associated protein 10
+分子 #29: U3 small nucleolar RNA-associated protein 15
+分子 #30: NET1-associated nuclear protein 1
+分子 #31: Periodic tryptophan protein 2
+分子 #32: U3 small nucleolar RNA-associated protein 12
+分子 #33: U3 small nucleolar RNA-associated protein 13
+分子 #34: U3 small nucleolar RNA-associated protein 18
+分子 #35: U3 small nucleolar RNA-associated protein 21
+分子 #36: U3 small nucleolar RNA-associated protein 6
+分子 #37: U3 small nucleolar RNA-associated protein 7
+分子 #38: U3 small nucleolar RNA-associated protein 11
+分子 #39: U3 small nucleolar RNA-associated protein MPP10
+分子 #40: U3 small nucleolar ribonucleoprotein protein IMP3
+分子 #41: U3 small nucleolar ribonucleoprotein protein IMP4
+分子 #42: Something about silencing protein 10
+分子 #43: Protein SOF1
+分子 #44: rRNA-processing protein FCF2
+分子 #45: rRNA-processing protein FCF1
+分子 #46: rRNA biogenesis protein RRP5
+分子 #47: U3 small nucleolar RNA-associated protein 22
+分子 #48: Ribosomal RNA-processing protein 7
+分子 #49: Ribosomal RNA small subunit methyltransferase NEP1
+分子 #50: Ribosome biogenesis protein BMS1
+分子 #51: RNA 3'-terminal phosphate cyclase-like protein
+分子 #52: Nucleolar complex protein 14
+分子 #53: U3 small nucleolar RNA-associated protein 20
+分子 #54: U3 small nucleolar RNA-associated protein 14
+分子 #55: Pno1
+分子 #56: Unassigned helices
+分子 #57: ZINC ION
+分子 #58: GUANOSINE-5'-TRIPHOSPHATE
+分子 #59: MAGNESIUM 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 2.0 mg/mL | |||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 10 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 45 sec. / 前処理 - 雰囲気: OTHER | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
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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: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - 画像ごとのフレーム数: 1-32 / 撮影したグリッド数: 10 / 実像数: 18028 / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.5 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |