+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12910 | |||||||||
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タイトル | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C | |||||||||
マップデータ | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, full map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 有糸分裂 / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 有糸分裂 / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / Antigen processing: Ubiquitination & Proteasome degradation / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / 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) / maturation of 5.8S rRNA / proteasome binding / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / ATPase activator activity / 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) / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / chromosome organization / regulation of translational fidelity / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / proteasome complex / small-subunit processome / assembly of large subunit precursor of preribosome / nuclear periphery / cytosolic ribosome assembly / maintenance of translational fidelity / オートファジー / protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / 核膜 / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / ATPase binding / negative regulation of translation / RNA helicase activity / rRNA binding / リボソーム / ヘリカーゼ / structural constituent of ribosome / 翻訳 (生物学) / mRNA binding / GTPase activity / GTP binding / 核小体 / ATP hydrolysis activity / DNA binding / RNA binding / 核質 / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Saccharomyces cerevisiae S288c (パン酵母) / Baker's yeast (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: 3.9 Å | |||||||||
データ登録者 | Milkereit P / Poell G | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: PLoS One / 年: 2021 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 |
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_12910.map.gz | 193.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12910-v30.xml emd-12910.xml | 68.5 KB 68.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12910_fsc.xml | 14.3 KB | 表示 | FSCデータファイル |
画像 | emd_12910.png | 126.5 KB | ||
その他 | emd_12910_half_map_1.map.gz emd_12910_half_map_2.map.gz | 193.6 MB 193.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12910 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12910 | HTTPS FTP |
-関連構造データ
関連構造データ | 7ohvMC 7of1C 7oh3C 7ohpC 7ohqC 7ohrC 7ohsC 7ohtC 7ohuC 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10780 (タイトル: Nog1-TAP associated immature ribosomal particles from S.cerevisae depleted of rpL2 Data size: 4.9 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae depleted of rpL2 [micrographs - multiframe]) |
-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_12910.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, 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_12910_half_map_1.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, 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_12910_half_map_2.map | ||||||||||||
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注釈 | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-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: ITS2
+分子 #4: Ribosome biogenesis protein BRX1
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4-A
+分子 #7: ATP-dependent RNA helicase HAS1
+分子 #8: 60S ribosomal protein L6-A
+分子 #9: 60S ribosomal protein L7-A
+分子 #10: 60S ribosomal protein L8-A
+分子 #11: 60S ribosomal protein L9-A
+分子 #12: rRNA-processing protein EBP2
+分子 #13: Proteasome-interacting protein CIC1
+分子 #14: 60S ribosomal protein L13-A
+分子 #15: 60S ribosomal protein L14-A
+分子 #16: 60S ribosomal protein L15-A
+分子 #17: 60S ribosomal protein L16-A
+分子 #18: 60S ribosomal protein L17-A
+分子 #19: 60S ribosomal protein L18-A
+分子 #20: 60S ribosomal protein L19-A
+分子 #21: 60S ribosomal protein L20-A
+分子 #22: 60S ribosomal protein L22-A
+分子 #23: 60S ribosomal protein L23-A
+分子 #24: Ribosome assembly factor MRT4
+分子 #25: 60S ribosomal protein L25
+分子 #26: 60S ribosomal protein L26-A
+分子 #27: 60S ribosomal protein L27-A
+分子 #28: 60S ribosomal protein L28
+分子 #29: Nucleolar GTP-binding protein 1
+分子 #30: 60S ribosomal protein L31-A
+分子 #31: 60S ribosomal protein L32
+分子 #32: 60S ribosomal protein L33-A
+分子 #33: 60S ribosomal protein L35-A
+分子 #34: 60S ribosomal protein L36-A
+分子 #35: 60S ribosomal protein L37-A
+分子 #36: 60S ribosomal protein L38
+分子 #37: Ribosome biogenesis protein ERB1
+分子 #38: Pescadillo homolog
+分子 #39: Ribosome biogenesis protein 15
+分子 #40: Ribosome biogenesis protein YTM1
+分子 #41: Ribosome biogenesis protein NSA2
+分子 #42: Ribosome biogenesis protein RLP7
+分子 #43: Ribosome biogenesis protein RLP24
+分子 #44: Nucleolar protein 16
+分子 #45: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #46: Eukaryotic translation initiation factor 6
+分子 #47: 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: 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 - 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 |
-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 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
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: 86.45 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |