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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 E2 nucleolar 60S ribosomal intermediate - Local Map for Noc2/Noc3 region | ||||||||||||
![]() | State E2 Noc2/Noc3 locally refined map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferases / nucleolus / RIBOSOME | ||||||||||||
機能・相同性 | ![]() 25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / 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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / nuclear pre-replicative complex / tRNA methylation / rRNA primary transcript binding / rRNA base methylation / protein folding chaperone complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / 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 / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / DNA replication initiation / mRNA transport / ribonucleoprotein complex binding / 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) / nuclear periphery / 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 / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / ribosome biogenesis / histone binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / structural constituent of ribosome / cell division / mRNA binding / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / 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: 3.17 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
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 | ![]() | 254.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 38.5 KB 38.5 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.9 KB | 表示 | ![]() |
画像 | ![]() | 92.7 KB | ||
Filedesc metadata | ![]() | 10.7 KB | ||
その他 | ![]() ![]() | 245.2 MB 243.7 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 884.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 884.2 KB | 表示 | |
XML形式データ | ![]() | 22.5 KB | 表示 | |
CIF形式データ | ![]() | 29.6 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 | ![]() 7r6kMC ![]() 7nacC ![]() 7nadC ![]() 7nafC ![]() 7r6qC ![]() 7r72C ![]() 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 E2 Noc2/Noc3 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 E2 Noc2/Noc3 locally refined half map 1
ファイル | emd_24280_half_map_1.map | ||||||||||||
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注釈 | State E2 Noc2/Noc3 locally refined 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: State E2 Noc2/Noc3 locally refined half map 2
ファイル | emd_24280_half_map_2.map | ||||||||||||
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注釈 | State E2 Noc2/Noc3 locally refined 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 : 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: 60S ribosomal subunit assembly/export protein LOC1
+分子 #3: Nucleolar complex protein 2
+分子 #4: Ribosome biogenesis protein BRX1
+分子 #5: 60S ribosomal protein L8-A
+分子 #6: Nucleolar complex-associated protein 3
+分子 #7: rRNA-processing protein EBP2
+分子 #8: 60S ribosomal protein L15-A
+分子 #9: 60S ribosomal protein L34-A
+分子 #10: 60S ribosomal protein L36-A
+分子 #11: 60S ribosome subunit biogenesis protein NIP7
+分子 #12: Ribosome biogenesis protein ERB1
+分子 #13: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+分子 #14: Ribosome biogenesis protein NSA2
+分子 #15: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #16: RRP17 isoform 1
-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 / 前処理 - タイプ: GLOW DISCHARGE | ||||||||||||||||||
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 |