+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-43021 | ||||||||||||
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タイトル | 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) | ||||||||||||
マップデータ | Overall map Dbp10 catalytic intermediate | ||||||||||||
試料 |
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キーワード | Ribosome biogenesis / intermediate DEAD-box ATPase / Ribosome-RNA complex | ||||||||||||
機能・相同性 | 機能・相同性情報 25S rRNA (cytosine2870-C5)-methyltransferase / 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) / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...25S rRNA (cytosine2870-C5)-methyltransferase / 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) / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / tRNA methylation / rRNA primary transcript binding / rRNA base methylation / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / protein folding chaperone complex / 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) / regulation of cell size / 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) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / mRNA transport / 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 / 90S preribosome / 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) / 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-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / ATPase binding / 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 / cell cycle / 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 | Saccharomyces cerevisiae BY4741 (パン酵母) / Saccharomyces cerevisiae BY4741-AV16 (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: 2.7 Å | ||||||||||||
データ登録者 | Cruz VE / Weirich CS / Peddada N / Erzberger JP | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2024 タイトル: The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis. 著者: Victor E Cruz / Christine S Weirich / Nagesh Peddada / Jan P Erzberger / 要旨: DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this ...DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit. | ||||||||||||
履歴 |
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-構造の表示
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 | emd_43021.map.gz | 229.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-43021-v30.xml emd-43021.xml | 76.5 KB 76.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_43021_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_43021.png | 105.7 KB | ||
Filedesc metadata | emd-43021.cif.gz | 18.5 KB | ||
その他 | emd_43021_half_map_1.map.gz emd_43021_half_map_2.map.gz | 194.9 MB 194.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-43021 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43021 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_43021_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_43021_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_43021_validation.xml.gz | 21.6 KB | 表示 | |
CIF形式データ | emd_43021_validation.cif.gz | 28.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43021 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43021 | 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_43021.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 | Overall map Dbp10 catalytic intermediate | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.08 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: Overall half-map 1 Dbp10 catalytic intermediate
ファイル | emd_43021_half_map_1.map | ||||||||||||
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注釈 | Overall half-map 1 Dbp10 catalytic intermediate | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Overall half-map 2 Dbp10 catalytic intermediate
ファイル | emd_43021_half_map_2.map | ||||||||||||
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注釈 | Overall half-map 2 Dbp10 catalytic intermediate | ||||||||||||
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 : 60S ribosome biogenesis intermediate
+超分子 #1: 60S ribosome biogenesis intermediate
+分子 #1: Saccharomyces cerevisiae 25S ribosomal RNA
+分子 #2: Saccharomyces cerevisiae 5.8S ribosomal RNA
+分子 #4: ITS2 RNA
+分子 #3: ATP-dependent RNA helicase DBP10
+分子 #5: 60S ribosomal subunit assembly/export protein LOC1
+分子 #6: Ribosomal RNA-processing protein 14
+分子 #7: Ribosome biogenesis protein BRX1
+分子 #8: Large ribosomal subunit protein uL3
+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: Large ribosomal subunit protein eL8A
+分子 #14: Large ribosomal subunit protein uL6A
+分子 #15: Ribosome biogenesis protein NSA1
+分子 #16: rRNA-processing protein EBP2
+分子 #17: Proteasome-interacting protein CIC1
+分子 #18: 60S ribosomal protein L13-A
+分子 #19: 60S ribosomal protein L14-A
+分子 #20: Large ribosomal subunit protein eL15A
+分子 #21: Large ribosomal subunit protein uL13A
+分子 #22: 60S ribosomal protein L17-A
+分子 #23: 60S ribosomal protein L18-A
+分子 #24: Protein MAK16
+分子 #25: Large ribosomal subunit protein eL20A
+分子 #26: Ribosomal RNA-processing protein 15
+分子 #27: 60S ribosomal protein L23-A
+分子 #28: Ribosome assembly factor MRT4
+分子 #29: 60S ribosomal protein L26-A
+分子 #30: Ribosome biogenesis protein SSF1
+分子 #31: Large ribosomal subunit protein uL1A
+分子 #32: Nucleolar GTP-binding protein 1
+分子 #33: 60S ribosomal protein L32
+分子 #34: 60S ribosomal protein L33-A
+分子 #35: 60S ribosomal protein L35-A
+分子 #36: 60S ribosomal protein L36-A
+分子 #37: 60S ribosomal protein L37-A
+分子 #38: 60S ribosome subunit biogenesis protein NIP7
+分子 #39: Ribosome biogenesis protein ERB1
+分子 #40: Pescadillo homolog
+分子 #41: Ribosome biogenesis protein 15
+分子 #42: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+分子 #43: Ribosome biogenesis protein NSA2
+分子 #44: Ribosome biogenesis protein RLP7
+分子 #45: Ribosome biogenesis protein RLP24
+分子 #46: Nucleolar protein 16
+分子 #47: Ribosomal RNA-processing protein 1
+分子 #48: Ribosome production factor 1
+分子 #49: Eukaryotic translation initiation factor 6
+分子 #50: GUANOSINE-5'-DIPHOSPHATE
+分子 #51: MAGNESIUM ION
+分子 #52: 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
濃度 | 0.5 mg/mL | |||||||||||||||
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緩衝液 | pH: 8 構成要素:
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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 |
-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: GATAN K3 (6k x 4k) / 平均電子線量: 39.3 e/Å2 |
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 FIELD / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 0.9 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |