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基本情報
登録情報 | データベース: EMDB / ID: EMD-12913 | |||||||||
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タイトル | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B | |||||||||
![]() | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B, full map | |||||||||
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![]() | ribosomal assembly state / RIBOSOME | |||||||||
機能・相同性 | ![]() positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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) ...positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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) / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / ribosomal subunit export from nucleus / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / ATPase binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
![]() | Milkereit P / Poell G | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. 著者: Gisela Pöll / Michael Pilsl / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit / ![]() 要旨: In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with ...In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 193 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 48.8 KB 48.8 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.2 KB | 表示 | ![]() |
画像 | ![]() | 91.9 KB | ||
Filedesc metadata | ![]() | 11.7 KB | ||
その他 | ![]() ![]() | 193.7 MB 193.7 MB | ||
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 | ![]() 7ohyMC ![]() 7of1C ![]() 7oh3C ![]() 7ohpC ![]() 7ohqC ![]() 7ohrC ![]() 7ohsC ![]() 7ohtC ![]() 7ohuC ![]() 7ohvC ![]() 7ohwC ![]() 7ohxC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 6.2 TB Data #1: Unaligned multi-frame migrographs of Nog1-TAP associated immature ribosomes depleted of rpL34 [micrographs - multiframe]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B, full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0635 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
-ハーフマップ: Nog1-TAP associated immature ribosomal particles from S. cerevisiae...
ファイル | emd_12913_half_map_1.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B, half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Nog1-TAP associated immature ribosomal particles from S. cerevisiae...
ファイル | emd_12913_half_map_2.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B, half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Nog1-TAP associated immature ribosomal particles from cells deple...
+超分子 #1: Nog1-TAP associated immature ribosomal particles from cells deple...
+分子 #1: 25S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: 60S ribosomal protein L3
+分子 #4: 60S ribosomal protein L4-A
+分子 #5: 60S ribosomal protein L6-A
+分子 #6: 60S ribosomal protein L7-A
+分子 #7: 60S ribosomal protein L8-A
+分子 #8: 60S ribosomal protein L9-A
+分子 #9: 60S ribosomal protein L13-A
+分子 #10: 60S ribosomal protein L14-A
+分子 #11: 60S ribosomal protein L15-A
+分子 #12: 60S ribosomal protein L16-A
+分子 #13: 60S ribosomal protein L17-A
+分子 #14: 60S ribosomal protein L18-A
+分子 #15: 60S ribosomal protein L20-A
+分子 #16: 60S ribosomal protein L23-A
+分子 #17: Ribosome assembly factor MRT4
+分子 #18: 60S ribosomal protein L26-A
+分子 #19: Nucleolar GTP-binding protein 1
+分子 #20: 60S ribosomal protein L32
+分子 #21: 60S ribosomal protein L33-A
+分子 #22: 60S ribosomal protein L35-A
+分子 #23: 60S ribosomal protein L37-A
+分子 #24: Ribosome biogenesis protein NSA2
+分子 #25: Ribosome biogenesis protein RLP24
+分子 #26: Eukaryotic translation initiation factor 6
+分子 #27: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 8 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 200 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.4 kPa | ||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 平均露光時間: 5.16 sec. / 平均電子線量: 88.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |