+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5jpq | ||||||
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タイトル | Cryo-EM structure of the 90S pre-ribosome | ||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / nuclear RNP | ||||||
機能・相同性 | 機能・相同性情報 tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / 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 / box C/D sno(s)RNA 3'-end processing ...tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / 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 / box C/D sno(s)RNA 3'-end processing / 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) / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA base methylation / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / N-acetyltransferase activity / rRNA methylation / U3 snoRNA binding / : / tRNA processing / 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 / snoRNA binding / 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 / 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 / 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 / RNA nuclease activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / small-subunit processome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / リボソーム生合成 / small ribosomal subunit / cytoplasmic translation / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / 核小体 / ATP hydrolysis activity / ミトコンドリア / RNA binding / 核質 / ATP binding / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Chaetomium thermophilum (菌類) 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: 7.3 Å | ||||||
データ登録者 | Turk, M. / Cheng, J. / Berninghausen, O. / Kornprobst, M. / Flemming, D. / Kos-Braun, I.C. / Kos, M. / Thoms, M. / Hurt, E. / Beckmann, R. | ||||||
引用 | ジャーナル: Cell / 年: 2016 タイトル: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. 著者: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt / 要旨: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding. | ||||||
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 | 5jpq.cif.gz | 2.7 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5jpq.ent.gz | 1.9 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5jpq.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jpq ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jpq | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+タンパク質 , 34種, 54分子 ABCDEFJKLNPlnGHIMOmQRSTUVWXYZa...
-RNA鎖 , 2種, 2分子 23
#35: RNA鎖 | 分子量: 579761.938 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Chaetomium thermophilum (菌類) |
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#36: RNA鎖 | 分子量: 87969.609 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Chaetomium thermophilum (菌類) |
-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 / タイプ: RIBOSOME / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: Chaetomium thermophilum (菌類) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 16 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 7.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 43000 / 対称性のタイプ: POINT |