+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11363 | |||||||||
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タイトル | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C | |||||||||
マップデータ | Multibody refine focus 3domain | |||||||||
試料 |
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キーワード | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
機能・相同性 | 機能・相同性情報 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / single-stranded telomeric DNA binding / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / 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 / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / snoRNA binding / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / 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) / enzyme activator activity / RNA endonuclease activity / nuclear periphery / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / helicase activity / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Saccharomyces cerevisiae S288C (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: 3.5 Å | |||||||||
データ登録者 | Cheng J / Lau B | |||||||||
引用 | ジャーナル: Science / 年: 2020 タイトル: 90 pre-ribosome transformation into the primordial 40 subunit. 著者: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / 要旨: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins. | |||||||||
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_11363.map.gz | 30.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11363-v30.xml emd-11363.xml | 57.1 KB 57.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11363_fsc.xml | 17 KB | 表示 | FSCデータファイル |
画像 | emd_11363.png | 78.2 KB | ||
Filedesc metadata | emd-11363.cif.gz | 15 KB | ||
その他 | emd_11363_additional.map.gz | 281.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11363 | 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_11363.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Multibody refine focus 3domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-追加マップ: Multibody refine focus 3domain
ファイル | emd_11363_additional.map | ||||||||||||
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注釈 | Multibody refine focus 3domain | ||||||||||||
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 : 90S pre-ribbosome state Dis-C
+超分子 #1: 90S pre-ribbosome state Dis-C
+分子 #1: Nucleolar complex protein 14
+分子 #2: Something about silencing protein 10
+分子 #3: Noc4,Nucleolar complex protein 4,Noc4
+分子 #4: rRNA-processing protein FCF1
+分子 #5: U3 small nucleolar ribonucleoprotein protein IMP4
+分子 #6: U3 small nucleolar RNA-associated protein MPP10
+分子 #7: Ribosome biogenesis protein BMS1
+分子 #8: RNA 3'-terminal phosphate cyclase-like protein
+分子 #9: Ribosomal RNA small subunit methyltransferase NEP1
+分子 #10: Essential nuclear protein 1
+分子 #11: Dimethyladenosine transferase
+分子 #12: Pre-rRNA-processing protein PNO1
+分子 #13: Rps5p
+分子 #14: 40S ribosomal protein S16-A
+分子 #15: 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18
+分子 #16: 40S ribosomal protein S19-A
+分子 #17: 40S ribosomal protein S28-A
+分子 #19: 40S ribosomal protein S1-A
+分子 #20: 40S ribosomal protein S4-A
+分子 #21: 40S ribosomal protein S6-A
+分子 #22: 40S ribosomal protein S7-A
+分子 #23: 40S ribosomal protein S8-A
+分子 #24: 40S ribosomal protein S9-A
+分子 #25: 40S ribosomal protein S11-A
+分子 #26: 40S ribosomal protein S13
+分子 #27: 40S ribosomal protein S14-A
+分子 #28: 40S ribosomal protein S25-A
+分子 #29: 40S ribosomal protein S22-A
+分子 #30: 40S ribosomal protein S23-A
+分子 #31: 40S ribosomal protein S24-A
+分子 #32: 40S ribosomal protein S27-A
+分子 #33: U3 small nucleolar RNA-associated protein 14
+分子 #34: Probable ATP-dependent RNA helicase DHR1
+分子 #18: 18S rRNA
+分子 #35: U3 snoRNA
+分子 #36: Poly-U RNA
+分子 #37: ZINC ION
+分子 #38: GUANOSINE-5'-TRIPHOSPHATE
+分子 #39: 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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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: 7.4 |
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グリッド | モデル: Quantifoil / 材質: COPPER / 支持フィルム - 材質: CARBON |
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: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 44.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |