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基本情報
登録情報 | データベース: EMDB / ID: EMD-12911 | |||||||||
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タイトル | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B | |||||||||
![]() | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B, full map | |||||||||
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![]() | ribosomal assembly state / RIBOSOME | |||||||||
機能・相同性 | ![]() snoRNA release from pre-rRNA / nuclear division / 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 / ATP-dependent activity, acting on RNA / rRNA primary transcript binding / 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) / preribosome, small subunit precursor ...snoRNA release from pre-rRNA / nuclear division / 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 / ATP-dependent activity, acting on RNA / rRNA primary transcript binding / 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) / preribosome, small subunit precursor / proteasome binding / maturation of 5.8S rRNA / 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 / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / translation initiation factor activity / maturation of LSU-rRNA / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / nuclear envelope / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 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: 3.5 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. | |||||||||
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構造の表示
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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 | ![]() | 193.3 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 66.9 KB 66.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.2 KB | 表示 | ![]() |
画像 | ![]() | 109.2 KB | ||
Filedesc metadata | ![]() | 15.7 KB | ||
その他 | ![]() ![]() | 193.7 MB 193.7 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 21.8 KB | 表示 | |
CIF形式データ | ![]() | 28.4 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 | ![]() 7ohwMC ![]() 7of1C ![]() 7oh3C ![]() 7ohpC ![]() 7ohqC ![]() 7ohrC ![]() 7ohsC ![]() 7ohtC ![]() 7ohuC ![]() 7ohvC ![]() 7ohxC ![]() 7ohyC 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: 7.4 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae depleted of rpL25 [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 rpL25 expression shut down, population B, full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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_12911_half_map_1.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 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_12911_half_map_2.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 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 #6: ITS2
+分子 #3: Protein MAK16
+分子 #4: Ribosomal RNA-processing protein 1
+分子 #5: Ribosome biogenesis protein NSA1
+分子 #7: Ribosome biogenesis protein BRX1
+分子 #8: 60S ribosomal protein L3
+分子 #9: 60S ribosomal protein L4-A
+分子 #10: ATP-dependent RNA helicase HAS1
+分子 #11: 60S ribosomal protein L6-A
+分子 #12: 60S ribosomal protein L7-A
+分子 #13: 60S ribosomal protein L8-A
+分子 #14: 60S ribosomal protein L9-A
+分子 #15: rRNA-processing protein EBP2
+分子 #16: Proteasome-interacting protein CIC1
+分子 #17: 60S ribosomal protein L13-A
+分子 #18: 60S ribosomal protein L14-A
+分子 #19: 60S ribosomal protein L15-A
+分子 #20: 60S ribosomal protein L16-A
+分子 #21: 60S ribosomal protein L17-A
+分子 #22: 60S ribosomal protein L18-A
+分子 #23: 60S ribosomal protein L20-A
+分子 #24: 60S ribosomal protein L23-A
+分子 #25: Ribosome assembly factor MRT4
+分子 #26: 60S ribosomal protein L26-A
+分子 #27: Nucleolar GTP-binding protein 1
+分子 #28: 60S ribosomal protein L32
+分子 #29: 60S ribosomal protein L33-A
+分子 #30: 60S ribosomal protein L35-A
+分子 #31: 60S ribosomal protein L36-A
+分子 #32: 60S ribosomal protein L37-A
+分子 #33: Ribosome biogenesis protein ERB1
+分子 #34: Pescadillo homolog
+分子 #35: Ribosome biogenesis protein 15
+分子 #36: Ribosome biogenesis protein NSA2
+分子 #37: Ribosome biogenesis protein RLP7
+分子 #38: Nucleolar protein 16
+分子 #39: Ribosome production factor 1
+分子 #40: Eukaryotic translation initiation factor 6
+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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![]() | 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: 86.09 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 |