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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-12905 | |||||||||
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タイトル | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae | |||||||||
![]() | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, full map | |||||||||
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![]() | ribosomal assembly state / RIBOSOME | |||||||||
機能・相同性 | ![]() protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / 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) / pre-mRNA 5'-splice site binding ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / 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) / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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) / translation initiation factor activity / proteasome complex / nuclear periphery / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / ATPase binding / 5S rRNA 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 / 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: 3.1 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 | ![]() | 193.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 83.4 KB 83.4 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.2 KB | 表示 | ![]() |
画像 | ![]() | 122.9 KB | ||
Filedesc metadata | ![]() | 17.2 KB | ||
その他 | ![]() ![]() | 194.2 MB 194.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 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 | ![]() 7ohqMC ![]() 7of1C ![]() 7oh3C ![]() 7ohpC ![]() 7ohrC ![]() 7ohsC ![]() 7ohtC ![]() 7ohuC ![]() 7ohvC ![]() 7ohwC ![]() 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: 8.3 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae [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 particle population C from S. cerevisiae, 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 particle population C from...
ファイル | emd_12905_half_map_1.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, 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 particle population C from...
ファイル | emd_12905_half_map_2.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, 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.
+超分子 #1: Nog1-TAP associated immature ribosomal particles.
+分子 #1: 25S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: 5S rRNA
+分子 #5: ITS2
+分子 #4: rRNA-processing protein CGR1
+分子 #6: 60S ribosomal protein L2-A
+分子 #7: 60S ribosomal protein L3
+分子 #8: 60S ribosomal protein L4-A
+分子 #9: 60S ribosomal protein L5
+分子 #10: 60S ribosomal protein L6-A
+分子 #11: 60S ribosomal protein L7-A
+分子 #12: 60S ribosomal protein L8-A
+分子 #13: 60S ribosomal protein L9-A
+分子 #14: 60S ribosomal protein L11-A
+分子 #15: Proteasome-interacting protein CIC1
+分子 #16: 60S ribosomal protein L13-A
+分子 #17: 60S ribosomal protein L14-A
+分子 #18: 60S ribosomal protein L15-A
+分子 #19: 60S ribosomal protein L16-A
+分子 #20: 60S ribosomal protein L17-A
+分子 #21: 60S ribosomal protein L18-A
+分子 #22: 60S ribosomal protein L19-A
+分子 #23: 60S ribosomal protein L20-A
+分子 #24: 60S ribosomal protein L21-A
+分子 #25: 60S ribosomal protein L22-A
+分子 #26: 60S ribosomal protein L23-A
+分子 #27: Ribosome assembly factor MRT4
+分子 #28: 60S ribosomal protein L25
+分子 #29: 60S ribosomal protein L26-A
+分子 #30: 60S ribosomal protein L27-A
+分子 #31: 60S ribosomal protein L28
+分子 #32: Nucleolar GTP-binding protein 1
+分子 #33: 60S ribosomal protein L30
+分子 #34: 60S ribosomal protein L31-A
+分子 #35: 60S ribosomal protein L32
+分子 #36: 60S ribosomal protein L33-A
+分子 #37: 60S ribosomal protein L34-A
+分子 #38: 60S ribosomal protein L35-A
+分子 #39: 60S ribosomal protein L36-A
+分子 #40: 60S ribosomal protein L37-A
+分子 #41: 60S ribosomal protein L38
+分子 #42: 60S ribosomal protein L39
+分子 #43: Nucleolar GTP-binding protein 2
+分子 #44: Pescadillo homolog
+分子 #45: Ribosome biogenesis protein 15
+分子 #46: 60S ribosomal protein L43-A
+分子 #47: Ribosome biogenesis protein NOP53
+分子 #48: Ribosome biogenesis protein NSA2
+分子 #49: Nuclear GTP-binding protein NUG1
+分子 #50: Ribosome biogenesis protein RLP7
+分子 #51: Ribosome biogenesis protein RLP24
+分子 #52: Ribosome biogenesis protein RPF2
+分子 #53: Regulator of ribosome biosynthesis
+分子 #54: Ribosome assembly protein 4
+分子 #55: Eukaryotic translation initiation factor 6
+分子 #56: UPF0642 protein YBL028C
+分子 #57: MAGNESIUM ION
+分子 #58: 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: 84.67 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 |