+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2528 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Arx1 pre-60S particle | |||||||||
マップデータ | Cryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP. | |||||||||
試料 |
| |||||||||
キーワード | ribosome biogenesis / ribosome assembly / pre-60S / 5S RNP / assembly intermediate | |||||||||
機能・相同性 | 機能・相同性情報 protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 加水分解酵素 / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 加水分解酵素 / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / nuclear-transcribed mRNA catabolic process / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / Neutrophil degranulation / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / host cell nucleus / nucleolus / proteolysis / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 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: 8.7 Å | |||||||||
データ登録者 | Leidig C / Thoms M / Holdermann I / Bradatsch B / Berninghausen O / Bange G / Sinning I / Hurt E / Beckmann R | |||||||||
引用 | ジャーナル: Nat Commun / 年: 2014 タイトル: 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle. 著者: Christoph Leidig / Matthias Thoms / Iris Holdermann / Bettina Bradatsch / Otto Berninghausen / Gert Bange / Irmgard Sinning / Ed Hurt / Roland Beckmann / 要旨: During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed ...During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature assembly states of rRNAs and their structural rearrangement during ribosome biogenesis. Using cryo-EM we characterize a pre-60S particle, where the 5S rRNA and its associated ribosomal proteins L18 and L5 (5S ribonucleoprotein (RNP)) are rotated by almost 180° when compared with the mature subunit. Consequently, neighbouring 25S rRNA helices that protrude from the base of the central protuberance are deformed. This altered topology is stabilized by nearby assembly factors (Rsa4 and Nog1), which were identified by fitting their three-dimensional structures into the cryo-EM density. We suggest that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_2528.map.gz | 39.1 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-2528-v30.xml emd-2528.xml | 12.6 KB 12.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_2528.png | 176.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2528 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2528_validation.pdf.gz | 370.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_2528_full_validation.pdf.gz | 370.2 KB | 表示 | |
XML形式データ | emd_2528_validation.xml.gz | 7.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2528 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2528 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_2528.map.gz / 形式: CCP4 / 大きさ: 264.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Cryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : TAP purification of Alb1-TAP from yeast.
全体 | 名称: TAP purification of Alb1-TAP from yeast. |
---|---|
要素 |
|
-超分子 #1000: TAP purification of Alb1-TAP from yeast.
超分子 | 名称: TAP purification of Alb1-TAP from yeast. / タイプ: sample / ID: 1000 / Number unique components: 1 |
---|
-超分子 #1: Arx1 pre-60S particle
超分子 | 名称: Arx1 pre-60S particle / タイプ: complex / ID: 1 / 組換発現: No Ribosome-details: ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S |
---|---|
由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Baker's Yeast |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: FEI VITROBOT MARK IV |
---|
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
日付 | 2012年11月12日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) 実像数: 5686 / 平均電子線量: 20 e/Å2 |
電子線 | 加速電圧: 200 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 FIELD |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 8.7 Å / 解像度の算出法: OTHER / 使用した粒子像数: 75887 |
---|
-原子モデル構築 1
初期モデル | PDB ID: 3u5d Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 3 / Chain - #2 - Chain ID: 4 |
---|---|
詳細 | The coordinates were initially fitted by rigid body fitting before the structure was manually adjusted to the density and refined using molecular dynamics simulations. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4v7f: |
-原子モデル構築 2
初期モデル | PDB ID: 3u5e Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: J / Chain - #9 - Chain ID: L / Chain - #10 - Chain ID: M / Chain - #11 - Chain ID: N / Chain - #12 - Chain ID: O / Chain - #13 - Chain ID: P / Chain - #14 - Chain ID: Q / Chain - #15 - Chain ID: R / Chain - #16 - Chain ID: S / Chain - #17 - Chain ID: T / Chain - #18 - Chain ID: U / Chain - #19 - Chain ID: V / Chain - #20 - Chain ID: X / Chain - #21 - Chain ID: Y / Chain - #22 - Chain ID: Z / Chain - #23 - Chain ID: a / Chain - #24 - Chain ID: c / Chain - #25 - Chain ID: d / Chain - #26 - Chain ID: e / Chain - #27 - Chain ID: f / Chain - #28 - Chain ID: g / Chain - #29 - Chain ID: h / Chain - #30 - Chain ID: i / Chain - #31 - Chain ID: j / Chain - #32 - Chain ID: k / Chain - #33 - Chain ID: l / Chain - #34 - Chain ID: p |
---|---|
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4v7f: |
-原子モデル構築 3
初期モデル | PDB ID: 3izs Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: J |
---|---|
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4v7f: |
-原子モデル構築 4
初期モデル | PDB ID: 4b6a Chain - Chain ID: t |
---|---|
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-4v7f: |