+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11809 | |||||||||
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タイトル | Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome, Dhr1-Dim1) | |||||||||
マップデータ | local resolution filtered map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / mRNA modification / Noc4p-Nop14p complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / mRNA modification / Noc4p-Nop14p complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CUT catabolic process / CURI complex / UTP-C complex / U4 snRNA 3'-end processing / rRNA 2'-O-methylation / nuclear polyadenylation-dependent rRNA catabolic process / Pwp2p-containing subcomplex of 90S preribosome / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / 3'-5' RNA helicase activity / 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 / rRNA catabolic process / tRNA export from nucleus / regulation of transcription by RNA polymerase I / nuclear mRNA surveillance / 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 / nonfunctional rRNA decay / 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 / poly(A) binding / 90S preribosome assembly / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / mTORC1-mediated signalling / RNA catabolic process / ヒドロキシル化 / rRNA methylation / poly(U) RNA binding / 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 / maturation of 5.8S rRNA / rRNA metabolic process / 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 / mRNA catabolic process 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: 7.5 Å | |||||||||
データ登録者 | Cheng J / Lau B / Venuta GL / Berninghausen O / Beckmann R / Hurt E | |||||||||
引用 | ジャーナル: Mol Cell / 年: 2021 タイトル: Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome. 著者: Benjamin Lau / Jingdong Cheng / Dirk Flemming / Giuseppe La Venuta / Otto Berninghausen / Roland Beckmann / Ed Hurt / 要旨: Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in ...Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis. | |||||||||
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_11809.map.gz | 242.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11809-v30.xml emd-11809.xml | 18.4 KB 18.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11809_fsc.xml | 17.2 KB | 表示 | FSCデータファイル |
画像 | emd_11809.png | 178.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11809 | 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_11809.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 | local resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1...
全体 | 名称: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample |
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要素 |
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-超分子 #1: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1...
超分子 | 名称: 90S-exosome super-complex in state Post-A1-exosome from Dhr1-Dim1 sample タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#77 |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
-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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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 | 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: CTFFIND |
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初期 角度割当 | タイプ: OTHER / 詳細: Relion |
最終 角度割当 | タイプ: OTHER / 詳細: Relion |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 7.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 3892 |
FSC曲線 (解像度の算出) |
-原子モデル構築 1
初期モデル | PDB ID: |
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精密化 | プロトコル: RIGID BODY FIT |