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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-0370 | ||||||||||||||||||
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タイトル | Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit | ||||||||||||||||||
![]() | Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit | ||||||||||||||||||
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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) / 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) / response to cycloheximide / 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 ...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) / response to cycloheximide / 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) / 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 / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translation initiation factor activity / 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 / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / nucleoplasm / 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: 3.6 Å | ||||||||||||||||||
![]() | Zhou Y / Musalgaonkar S / Johnson AW / Taylor DW | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. 著者: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor / ![]() 要旨: The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the ...The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome. | ||||||||||||||||||
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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-EMDBアーカイブ
マップデータ | ![]() | 203 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 64.2 KB 64.2 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.7 KB | 表示 | ![]() |
画像 | ![]() | 178.5 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 601.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 601.2 KB | 表示 | |
XML形式データ | ![]() | 13.6 KB | 表示 | |
CIF形式データ | ![]() | 18.4 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 | ![]() 6n8kMC ![]() 0369C ![]() 0371C ![]() 0372C ![]() 0373C ![]() 0374C ![]() 6n8jC ![]() 6n8lC ![]() 6n8mC ![]() 6n8nC ![]() 6n8oC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ |
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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 | Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1 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
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試料の構成要素
+全体 : Early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit
+超分子 #1: Early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit
+分子 #1: Ribosomal Protein uL1
+分子 #2: 60S ribosomal export protein NMD3
+分子 #3: 60S ribosomal protein L2-A
+分子 #4: 60S ribosomal protein L28
+分子 #5: 60S ribosomal protein L3
+分子 #6: Nucleolar GTP-binding protein 1
+分子 #7: 60S ribosomal protein L4-A
+分子 #8: 60S ribosomal protein L30
+分子 #9: 60S ribosomal protein L31-A
+分子 #10: 60S ribosomal protein L6-A
+分子 #11: 60S ribosomal protein L32
+分子 #12: 60S ribosomal protein L7-A
+分子 #13: 60S ribosomal protein L33-A
+分子 #14: 60S ribosomal protein L8-A
+分子 #15: 60S ribosomal protein L34-A
+分子 #16: Bud site selection protein 20
+分子 #17: 60S ribosomal protein L9-A
+分子 #18: 60S ribosomal protein L35-A
+分子 #19: 60S ribosomal protein L36-A
+分子 #20: 60S ribosomal protein L37-A
+分子 #21: 60S ribosomal protein L38
+分子 #22: 60S ribosomal protein L13-A
+分子 #23: 60S ribosomal protein L39
+分子 #24: 60S ribosomal protein L14-A
+分子 #25: 60S ribosomal protein L43-A
+分子 #26: 60S ribosomal protein L15-A
+分子 #27: Ribosome biogenesis protein RLP24
+分子 #28: 60S ribosomal protein L16-A
+分子 #29: 60S ribosomal protein L17-A
+分子 #30: 60S ribosomal protein L18-A
+分子 #31: 60S ribosomal protein L19-A
+分子 #32: 60S ribosomal protein L20-A
+分子 #33: 60S ribosomal protein L21-A
+分子 #34: 60S ribosomal protein L22-A
+分子 #35: 60S ribosomal protein L23-A
+分子 #36: Ribosome assembly factor MRT4
+分子 #37: 60S ribosomal protein L25
+分子 #38: 60S ribosomal protein L26-A
+分子 #39: Eukaryotic translation initiation factor 6
+分子 #40: 60S ribosomal protein L27-A
+分子 #41: UPF0642 protein YBL028C
+分子 #42: 60S ribosomal protein L5
+分子 #43: 60S ribosomal protein L11-A
+分子 #44: 60S ribosomal protein L42-A
+分子 #45: 60S ribosomal protein L29
+分子 #46: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+分子 #47: 5S rRNA
+分子 #48: 5.8S rRNA
+分子 #49: GUANOSINE-5'-TRIPHOSPHATE
+分子 #50: MAGNESIUM 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: 7.5 |
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グリッド | 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 詳細: unspecified |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 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: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均露光時間: 6.0 sec. / 平均電子線量: 40.0 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: 100.0 µm / 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): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |