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データを開く
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基本情報
登録情報 | ![]() | ||||||||||||
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タイトル | State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 locally refined map | ||||||||||||
![]() | State E1 Spb4 locally refined map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
機能・相同性 | ![]() 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / PeBoW complex / nuclear pre-replicative complex ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / PeBoW complex / nuclear pre-replicative complex / 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) / rRNA methylation / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / DNA replication initiation / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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 / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / ribosome biogenesis / histone binding / ATPase binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / translation / cell division / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP 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: 3.07 Å | ||||||||||||
![]() | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. 著者: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger / ![]() ![]() ![]() 要旨: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly. | ||||||||||||
履歴 |
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構造の表示
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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 | ![]() | 254.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 47.5 KB 47.5 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.8 KB | 表示 | ![]() |
画像 | ![]() | 132 KB | ||
Filedesc metadata | ![]() | 11.9 KB | ||
その他 | ![]() ![]() | 251.2 MB 246.4 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 925.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 925 KB | 表示 | |
XML形式データ | ![]() | 22.6 KB | 表示 | |
CIF形式データ | ![]() | 29.7 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 | ![]() 7r72MC ![]() 7nacC ![]() 7nadC ![]() 7nafC ![]() 7r6kC ![]() 7r6qC ![]() 7r7aC ![]() 7r7cC ![]() 7u0hC 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 | 類似検索 - 機能・相同性 ![]() |
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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 | State E1 Spb4 locally refined map | ||||||||||||||||||||
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: State E1 Spb4 locally refined half map 2
ファイル | emd_24290_half_map_1.map | ||||||||||||
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注釈 | State E1 Spb4 locally refined half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: State E1 Spb4 locally refined half map 1
ファイル | emd_24290_half_map_2.map | ||||||||||||
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注釈 | State E1 Spb4 locally refined half map 1 | ||||||||||||
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 : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+超分子 #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+分子 #1: 25S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: Nucleolar complex protein 2
+分子 #4: 60S ribosomal protein L3
+分子 #5: 60S ribosomal protein L8-A
+分子 #6: Nucleolar complex-associated protein 3
+分子 #7: 60S ribosomal protein L17-A
+分子 #8: 60S ribosomal protein L19-A
+分子 #9: 60S ribosomal protein L22-A
+分子 #10: 60S ribosomal protein L25
+分子 #11: 60S ribosomal protein L27-A
+分子 #12: Nucleolar GTP-binding protein 1
+分子 #13: 60S ribosomal protein L30
+分子 #14: 60S ribosomal protein L31-A
+分子 #15: 60S ribosomal protein L34-A
+分子 #16: 60S ribosomal protein L37-A
+分子 #17: 60S ribosomal protein L38
+分子 #18: Ribosome biogenesis protein ERB1
+分子 #19: Pescadillo homolog
+分子 #20: Ribosome biogenesis protein YTM1
+分子 #21: Ribosome biogenesis protein RLP7
+分子 #22: Ribosome biogenesis protein RLP24
+分子 #23: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #24: ATP-dependent rRNA helicase SPB4
+分子 #25: 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
濃度 | 0.45 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 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: CONTINUOUS / 支持フィルム - Film thickness: 0.3 | ||||||||||||||||||
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: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 4523 / 平均露光時間: 0.05 sec. / 平均電子線量: 1.2 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 / 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 / 倍率(公称値): 81000 |
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 |
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画像解析
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | ![]() PDB-7r72: |