+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11357 | |||||||||
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タイトル | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Noc4p-Nop14p complex / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity ...Noc4p-Nop14p complex / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis / snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / ヒドロキシル化 / rRNA methylation / U3 snoRNA binding / : / poly(A)+ mRNA export from nucleus / 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 / preribosome, small subunit precursor / snoRNA binding / spliceosomal complex assembly / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / nucleolar large rRNA transcription by RNA polymerase I / 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 / enzyme activator activity / proteasome assembly / 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) / regulation of translational fidelity / 転写後修飾 / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / 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 / nuclear periphery / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / mRNA splicing, via spliceosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / unfolded protein binding / リボソーム生合成 / small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / 細胞周期 / 翻訳 (生物学) / mRNA binding / GTPase activity / GTP binding / 核小体 / ATP hydrolysis activity 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Baker's yeast (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: 4.4 Å | |||||||||
データ登録者 | Cheng J / Lau B / Venuta GL / Berninghausen O / Hurt E / Beckmann R | |||||||||
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_11357.map.gz | 44.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11357-v30.xml emd-11357.xml | 83.2 KB 83.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11357_fsc.xml | 17.1 KB | 表示 | FSCデータファイル |
画像 | emd_11357.png | 148.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11357 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11357 | 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_11357.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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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
-試料の構成要素
+全体 : 90S pre-ribbosome state A
+超分子 #1: 90S pre-ribbosome state A
+分子 #1: Periodic tryptophan protein 2
+分子 #2: Nucleolar complex protein 14
+分子 #3: Something about silencing protein 10
+分子 #4: U3 small nucleolar RNA-associated protein 4
+分子 #5: U3 small nucleolar RNA-associated protein 5
+分子 #6: U3 small nucleolar RNA-associated protein 6
+分子 #7: U3 small nucleolar RNA-associated protein 7
+分子 #8: U3 small nucleolar RNA-associated protein 8
+分子 #9: U3 small nucleolar RNA-associated protein 9
+分子 #10: U3 small nucleolar RNA-associated protein 10
+分子 #11: U3 small nucleolar RNA-associated protein 11
+分子 #12: U3 small nucleolar RNA-associated protein 12
+分子 #13: U3 small nucleolar RNA-associated protein 13
+分子 #14: U3 small nucleolar RNA-associated protein 14
+分子 #15: U3 small nucleolar RNA-associated protein 15
+分子 #16: Bud site selection protein 21
+分子 #17: NET1-associated nuclear protein 1
+分子 #18: U3 small nucleolar RNA-associated protein 18
+分子 #19: Nucleolar complex protein 4
+分子 #20: U3 small nucleolar RNA-associated protein 21
+分子 #21: U3 small nucleolar RNA-associated protein 22
+分子 #22: rRNA-processing protein FCF1
+分子 #23: Ribosome biogenesis protein UTP30
+分子 #24: rRNA 2'-O-methyltransferase fibrillarin
+分子 #25: Nucleolar protein 56
+分子 #26: Nucleolar protein 58
+分子 #27: 13 kDa ribonucleoprotein-associated protein
+分子 #28: Ribosomal RNA-processing protein 9
+分子 #29: U3 small nucleolar ribonucleoprotein protein IMP3
+分子 #30: U3 small nucleolar ribonucleoprotein protein IMP4
+分子 #31: U3 small nucleolar RNA-associated protein MPP10
+分子 #32: Ribosome biogenesis protein BMS1
+分子 #33: RNA 3'-terminal phosphate cyclase-like protein
+分子 #34: Ribosomal RNA-processing protein 7
+分子 #35: Ribosomal RNA small subunit methyltransferase NEP1
+分子 #36: Essential nuclear protein 1
+分子 #37: Pre-rRNA-processing protein PNO1
+分子 #38: rRNA-processing protein FCF2
+分子 #39: Protein FAF1
+分子 #40: KRR1 small subunit processome component
+分子 #41: Protein SOF1
+分子 #42: Regulator of rDNA transcription protein 14
+分子 #43: 40S ribosomal protein S1-A
+分子 #44: Rps5p
+分子 #45: 40S ribosomal protein S7-A
+分子 #46: 40S ribosomal protein S9-A
+分子 #47: 40S ribosomal protein S13
+分子 #48: 40S ribosomal protein S14-A
+分子 #49: 40S ribosomal protein S16-A
+分子 #50: 40S ribosomal protein S18-A
+分子 #51: 40S ribosomal protein S22-A
+分子 #52: 40S ribosomal protein S23-A
+分子 #53: 40S ribosomal protein S27-A
+分子 #54: 40S ribosomal protein S28-A
+分子 #55: 5ETS RNA
+分子 #56: 18S rRNA
+分子 #57: U3 snoRNA
+分子 #58: ZINC ION
+分子 #59: MAGNESIUM ION
+分子 #60: GUANOSINE-5'-TRIPHOSPHATE
-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 / 前処理 - タイプ: GLOW DISCHARGE |
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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | #0 - Image recording ID: 1 #0 - フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) #0 - 平均電子線量: 44.0 e/Å2 / #1 - Image recording ID: 2 #1 - フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) #1 - 平均電子線量: 44.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |