+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6lqv | |||||||||
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タイトル | Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) | |||||||||
要素 |
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キーワード | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 | |||||||||
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 / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / nuclear microtubule / t-UTP complex ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / nuclear microtubule / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / snRNA binding / mRNA modification / tRNA re-export from nucleus / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / regulation of transcription by RNA polymerase I / box C/D sno(s)RNA 3'-end processing / rDNA heterochromatin / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / tRNA export from nucleus / rRNA base methylation / rRNA primary transcript binding / SUMOylation of RNA binding proteins / O-methyltransferase activity / protein localization to nucleolus / small nuclear ribonucleoprotein complex / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U4 snRNP / 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 / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / 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 / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / RNA processing / 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) / vesicle-mediated transport / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / protein transport / peroxisome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) Saccharomyces cerevisiae (パン酵母) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.8 Å | |||||||||
データ登録者 | Du, Y. / Ye, K. | |||||||||
資金援助 | 中国, 2件
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引用 | ジャーナル: Science / 年: 2020 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 |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6lqv.cif.gz | 4.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6lqv.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6lqv.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6lqv_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6lqv_full_validation.pdf.gz | 2 MB | 表示 | |
XML形式データ | 6lqv_validation.xml.gz | 515.2 KB | 表示 | |
CIF形式データ | 6lqv_validation.cif.gz | 835.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/lq/6lqv ftp://data.pdbj.org/pub/pdb/validation_reports/lq/6lqv | HTTPS FTP |
-関連構造データ
関連構造データ | 0955MC 0949C 0950C 0951C 0952C 0953C 0954C 6lqpC 6lqqC 6lqrC 6lqsC 6lqtC 6lquC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+RNA鎖 , 3種, 3分子 3A5ASA
+40S ribosomal protein ... , 10種, 10分子 SFSGSHSJSKSMSRSYSZSd
+タンパク質 , 14種, 18分子 3B3C3F3G3HAGB15B5H5IRGRHRKRLRMRSRYX1
+Nucleolar protein ... , 2種, 2分子 3D3E
+U3 small nucleolar RNA-associated protein ... , 16種, 16分子 A4A5A8A9AEAFB2B3B8BEB65C5D5ERPRQ
+U3 small nucleolar ribonucleoprotein protein ... , 3種, 3分子 5F5GRB
+RRNA-processing protein ... , 2種, 2分子 5J5K
+Ribosome biogenesis protein ... , 2種, 2分子 RARJ
+Nucleolar complex protein ... , 2種, 2分子 RNRO
+非ポリマー , 3種, 3分子
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: 90S pre-ribosome (Dhr1-depleted, state C1) / タイプ: COMPLEX / Entity ID: #1-#54 / 由来: NATURAL | |||||||||||||||
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分子量 | 値: 5 MDa / 実験値: NO | |||||||||||||||
由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c | |||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | |||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 10 / 実像数: 18028 |
画像スキャン | 動画フレーム数/画像: 32 / 利用したフレーム数/画像: 1-32 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 382298 | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 9421 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6LQR Accession code: 6LQR / Source name: PDB / タイプ: experimental model |