+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-7445 | ||||||||||||||||||
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タイトル | Yeast nucleolar pre-60S ribosomal subunit (state 3) | ||||||||||||||||||
マップデータ | LSU processome state 3 | ||||||||||||||||||
試料 |
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キーワード | Pre-60S / ribosome biogenesis (リボソーム生合成) / LSU processome / ribosome (リボソーム) | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor ...snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / maturation of 5.8S rRNA / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / 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) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / proteasome complex / small-subunit processome / オートファジー / protein catabolic process / ribosomal small subunit biogenesis / rRNA processing / protein-macromolecule adaptor activity / large ribosomal subunit rRNA binding / リボソーム生合成 / 核膜 / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / リボソーム / rRNA binding / ヘリカーゼ / structural constituent of ribosome / 細胞周期 / mRNA binding / 核小体 / ATP hydrolysis activity / DNA binding / RNA binding / 核質 / ATP binding / metal ion binding / 細胞核 / identical protein binding / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae BY4741 (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: 4.6 Å | ||||||||||||||||||
データ登録者 | Sanghai ZA / Miller L | ||||||||||||||||||
資金援助 | 米国, スイス, 5件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Modular assembly of the nucleolar pre-60S ribosomal subunit. 著者: Zahra Assur Sanghai / Linamarie Miller / Kelly R Molloy / Jonas Barandun / Mirjam Hunziker / Malik Chaker-Margot / Junjie Wang / Brian T Chait / Sebastian Klinge / 要旨: Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly ...Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner. | ||||||||||||||||||
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_7445.map.gz | 388.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-7445-v30.xml emd-7445.xml | 60.4 KB 60.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_7445_fsc.xml | 17 KB | 表示 | FSCデータファイル |
画像 | emd_7445.png | 19.9 KB | ||
Filedesc metadata | emd-7445.cif.gz | 14 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-7445 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7445 | 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_7445.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 | LSU processome state 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.3 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 : Yeast nucleolar pre-60S ribosomal subunit
+超分子 #1: Yeast nucleolar pre-60S ribosomal subunit
+分子 #1: 35S pre-ribosomal RNA miscRNA
+分子 #2: 5.8S rRNA
+分子 #3: ITS2
+分子 #4: Ribosome biogenesis protein NSA1
+分子 #5: 60S ribosomal protein L4-A
+分子 #6: Protein MAK16
+分子 #7: 60S ribosomal protein L6-A
+分子 #8: 60S ribosomal protein L7-A
+分子 #9: 60S ribosomal protein L8-A
+分子 #10: Ribosome production factor 1
+分子 #11: Proteasome-interacting protein CIC1
+分子 #12: 60S ribosomal protein L13-A
+分子 #13: 60S ribosomal protein L14-A
+分子 #14: 60S ribosomal protein L15-A
+分子 #15: 60S ribosomal protein L16-A
+分子 #16: 60S ribosomal protein L17-A
+分子 #17: 60S ribosomal protein L18-A
+分子 #18: 60S ribosomal protein L20-A
+分子 #19: 60S ribosomal protein L25
+分子 #20: 60S ribosomal protein L26-A
+分子 #21: 60S ribosomal protein L27-A
+分子 #22: Nucleolar protein 16
+分子 #23: Ribosome biogenesis protein BRX1
+分子 #24: 60S ribosomal protein L30
+分子 #25: Ribosome biogenesis protein YTM1
+分子 #26: 60S ribosomal protein L32
+分子 #27: 60S ribosomal protein L33-A
+分子 #28: 60S ribosomal protein L34-A
+分子 #29: 60S ribosomal protein L35-A
+分子 #30: 60S ribosomal protein L36-A
+分子 #31: 60S ribosomal protein L37-A
+分子 #32: 60S ribosomal protein L38
+分子 #33: rRNA-processing protein EBP2
+分子 #34: Pescadillo homolog
+分子 #35: Ribosome biogenesis protein 15
+分子 #36: ATP-dependent RNA helicase HAS1
+分子 #37: Ribosome biogenesis protein ERB1
+分子 #38: Ribosome biogenesis protein RLP7
+分子 #39: BRX1 associated peptide
+分子 #40: Ribosomal RNA-processing protein 1
+分子 #41: ZINC ION
-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: 7.6 |
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グリッド | 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: LACEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 295 K / 装置: FEI VITROBOT MARK IV |
-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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 1.56 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
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得られたモデル | PDB-6cb1: |