+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10841 | |||||||||
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タイトル | pre-60S State NE1 (TAP-Flag-Nop53) | |||||||||
マップデータ | State NE1: pre-60S ribosomal subunit purified via Nop53 Local resolution filtered 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 / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / 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 ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / 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 / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / nuclear-transcribed mRNA catabolic process / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome complex / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / protein transport / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / protein-macromolecule adaptor activity / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / host cell nucleus / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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 | Kater L / Beckmann R | |||||||||
引用 | ジャーナル: Mol Cell / 年: 2020 タイトル: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. 著者: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt / 要旨: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression. | |||||||||
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_10841.map.gz | 126.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10841-v30.xml emd-10841.xml | 64.6 KB 64.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10841_fsc.xml | 13.7 KB | 表示 | FSCデータファイル |
画像 | emd_10841.png | 118.1 KB | ||
その他 | emd_10841_half_map_1.map.gz emd_10841_half_map_2.map.gz | 170.9 MB 170.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10841 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10841 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10841_validation.pdf.gz | 412.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10841_full_validation.pdf.gz | 411.6 KB | 表示 | |
XML形式データ | emd_10841_validation.xml.gz | 19.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10841 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10841 | 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_10841.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | State NE1: pre-60S ribosomal subunit purified via Nop53 Local resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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: Relion half map (unfiltered, unmasked)
ファイル | emd_10841_half_map_1.map | ||||||||||||
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注釈 | Relion half map (unfiltered, unmasked) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Relion half map (unfiltered, unmasked)
ファイル | emd_10841_half_map_2.map | ||||||||||||
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注釈 | Relion half map (unfiltered, unmasked) | ||||||||||||
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 : pre-60S assembly state NE1
+超分子 #1: pre-60S assembly state NE1
+分子 #1: 60S ribosomal protein L3
+分子 #2: 60S ribosomal protein L4-A
+分子 #3: 60S ribosomal protein L6-A
+分子 #4: 60S ribosomal protein L7-A
+分子 #5: 60S ribosomal protein L8-A
+分子 #6: 60S ribosomal protein L9-A
+分子 #7: Proteasome-interacting protein CIC1
+分子 #8: 60S ribosomal protein L13-A
+分子 #9: 60S ribosomal protein L14-A
+分子 #10: 60S ribosomal protein L15-A
+分子 #11: 60S ribosomal protein L16-A
+分子 #12: 60S ribosomal protein L17-A
+分子 #13: 60S ribosomal protein L18-A
+分子 #14: 60S ribosomal protein L19-A
+分子 #15: 60S ribosomal protein L20-A
+分子 #16: 60S ribosomal protein L21-A
+分子 #17: 60S ribosomal protein L22-A
+分子 #18: 60S ribosomal protein L23-A
+分子 #19: Ribosome assembly factor MRT4
+分子 #20: 60S ribosomal protein L25
+分子 #21: 60S ribosomal protein L26-A
+分子 #22: 60S ribosomal protein L27-A
+分子 #23: 60S ribosomal protein L28
+分子 #24: Nucleolar GTP-binding protein 1
+分子 #25: 60S ribosomal protein L30
+分子 #26: 60S ribosomal protein L31-A
+分子 #27: 60S ribosomal protein L32
+分子 #28: 60S ribosomal protein L33-A
+分子 #29: 60S ribosomal protein L34-A
+分子 #30: 60S ribosomal protein L35-A
+分子 #31: 60S ribosomal protein L36-A
+分子 #32: 60S ribosomal protein L37-A
+分子 #33: 60S ribosomal protein L38
+分子 #34: 60S ribosomal protein L39
+分子 #35: Pescadillo homolog
+分子 #36: Ribosome biogenesis protein 15
+分子 #37: Ribosome biogenesis protein NOP53
+分子 #38: Ribosome biogenesis protein NSA2
+分子 #39: Nuclear GTP-binding protein NUG1
+分子 #40: Ribosome biogenesis protein RLP7
+分子 #41: Ribosome biogenesis protein RLP24
+分子 #42: Eukaryotic translation initiation factor 6
+分子 #43: UPF0642 protein YBL028C
+分子 #47: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #44: 25S rRNA
+分子 #45: 5.8S rRNA
+分子 #46: ITS2
-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: 7.5 |
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グリッド | モデル: Quantifoil R3/3 / 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 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / 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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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - サンプリング間隔: 14.0 µm / デジタル化 - 画像ごとのフレーム数: 1-10 / 撮影したグリッド数: 2 / 平均電子線量: 24.0 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 |
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 |