+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6lqr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of 90S small subunit preribosomes in transition states (State C) | |||||||||
![]() |
| |||||||||
![]() | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 | |||||||||
機能・相同性 | ![]() mRNA modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process ...mRNA modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / tRNA wobble cytosine modification / rRNA 2'-O-methylation / CURI complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / UTP-C complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear microtubule / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / snRNA binding / positive regulation of RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / 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) / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / U4/U6 snRNP / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / O-methyltransferase activity / small nuclear ribonucleoprotein complex / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / poly(U) RNA binding / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U4 snRNP / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / U3 snoRNA binding / 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 / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / 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 / regulation of translational fidelity / Ub-specific processing proteases / RNA processing / ribosomal subunit export from nucleus / Cajal body / 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 / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / protein transport / ribosome biogenesis / ribosomal small subunit biogenesis 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
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: 8.6 Å | |||||||||
![]() | Du, Y. / Ye, K. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | 分子: ![]() ![]() |
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 4.9 MB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.7 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.8 MB | 表示 | |
XML形式データ | ![]() | 534.1 KB | 表示 | |
CIF形式データ | ![]() | 906.5 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 | ![]() 0951MC ![]() 0949C ![]() 0950C ![]() 0952C ![]() 0953C ![]() 0954C ![]() 0955C ![]() 6lqpC ![]() 6lqqC ![]() 6lqsC ![]() 6lqtC ![]() 6lquC ![]() 6lqvC 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 ( |
---|---|
類似構造データ |
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
+RNA鎖 , 3種, 3分子 3A5ASA
+40S ribosomal protein ... , 16種, 16分子 SCSFSGSHSISJSKSMSOSPSRSXSYSZScSd
+タンパク質 , 15種, 19分子 3B3C3G3HAGB15B5H5IRDRGRHRKRLRMRSRTRYX1
+Nucleolar protein ... , 2種, 2分子 3D3E
+Ribosomal RNA-processing protein ... , 2種, 2分子 3FRF
+U3 small nucleolar RNA-associated protein ... , 17種, 17分子 A4A5A8A9AEAFB2B3B8BEB65C5D5ERERPRQ
+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, 4分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 C) / タイプ: COMPLEX / Entity ID: #1-#64 / 由来: NATURAL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 値: 5 MDa / 実験値: NO | |||||||||||||||
由来(天然) | 生物種: ![]() ![]() 株: ATCC 204508 / S288c | |||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||
緩衝液成分 |
| |||||||||||||||
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 |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
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 |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 8.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 3050 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6LQP Accession code: 6LQP / Source name: PDB / タイプ: experimental model |