+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14471 | |||||||||
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タイトル | Structure of pre-60S particle bound to DRG1(AFG2) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Ribosome biogenesis / AAA-ATPases / large ribosomal subunit / substrate recognition / substrate translocation mechanism / single particle cryo-EM / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 加水分解酵素 / positive regulation of ATP-dependent activity / protein hexamerization / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / response to cycloheximide / maturation of 5.8S rRNA / non-chaperonin molecular chaperone ATPase / SRP-dependent cotranslational protein targeting to membrane ...加水分解酵素 / positive regulation of ATP-dependent activity / protein hexamerization / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / response to cycloheximide / maturation of 5.8S rRNA / non-chaperonin molecular chaperone ATPase / 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 / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / protein transport / ribosome biogenesis / ATPase binding / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to xenobiotic stimulus / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) / Saccharomyces cerevisiae S288C ATCC 204508 / S288c (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: 3.8 Å | |||||||||
データ登録者 | Prattes M / Grishkovskaya I / Bergler H / Haselbach D | |||||||||
資金援助 | オーストリア, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2022 タイトル: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. 著者: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Christina Hetzmannseder / Gertrude Zisser / Carolin Sailer / Vasileios Kargas / Mathias Loibl / Magdalena Gerhalter / Lisa ...著者: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Christina Hetzmannseder / Gertrude Zisser / Carolin Sailer / Vasileios Kargas / Mathias Loibl / Magdalena Gerhalter / Lisa Kofler / Alan J Warren / Florian Stengel / David Haselbach / Helmut Bergler / 要旨: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from ...The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases. | |||||||||
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_14471.map.gz | 387.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14471-v30.xml emd-14471.xml | 77.2 KB 77.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_14471.png | 49 KB | ||
その他 | emd_14471_half_map_1.map.gz emd_14471_half_map_2.map.gz | 390.9 MB 390.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14471 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14471 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14471_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14471_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_14471_validation.xml.gz | 18.1 KB | 表示 | |
CIF形式データ | emd_14471_validation.cif.gz | 21.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14471 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14471 | HTTPS FTP |
-関連構造データ
関連構造データ | 7z34MC 7z11C C: 同じ文献を引用 (文献) 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F&H 検索 |
-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_14471.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.3375 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: #2
ファイル | emd_14471_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_14471_half_map_2.map | ||||||||||||
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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 ribosomal particle in complex with DRG1(AFG2)
+超分子 #1: pre-60S ribosomal particle in complex with DRG1(AFG2)
+分子 #1: ATPase family gene 2 protein
+分子 #5: Probable metalloprotease ARX1
+分子 #6: 60S ribosomal protein L2-A
+分子 #7: 60S ribosomal protein L3
+分子 #8: 60S ribosomal protein L4-A
+分子 #9: 60S ribosomal protein L5
+分子 #10: 60S ribosomal protein L6-A
+分子 #11: 60S ribosomal protein L7-A
+分子 #12: 60S ribosomal protein L8-A
+分子 #13: 60S ribosomal protein L9-A
+分子 #14: Bud site selection protein 20
+分子 #15: 60S ribosomal protein L11-A
+分子 #16: 60S ribosomal protein L28
+分子 #17: 60S ribosomal protein L13-A
+分子 #18: 60S ribosomal protein L14-A
+分子 #19: 60S ribosomal protein L15-A
+分子 #20: 60S ribosomal protein L16-A
+分子 #21: 60S ribosomal protein L17-A
+分子 #22: 60S ribosomal protein L18-A
+分子 #23: 60S ribosomal protein L19-A
+分子 #24: 60S ribosomal protein L20-A
+分子 #25: 60S ribosomal protein L21-A
+分子 #26: 60S ribosomal protein L22-A
+分子 #27: 60S ribosomal protein L23-A
+分子 #28: Ribosome assembly factor MRT4
+分子 #29: 60S ribosomal protein L25
+分子 #30: 60S ribosomal protein L26-A
+分子 #31: 60S ribosomal protein L27-A
+分子 #32: 60S ribosomal protein L12-A
+分子 #33: Nucleolar GTP-binding protein 1
+分子 #34: 60S ribosomal protein L30
+分子 #35: 60S ribosomal protein L31-A
+分子 #36: 60S ribosomal protein L32
+分子 #37: 60S ribosomal protein L33-A
+分子 #38: 60S ribosomal protein L34-A
+分子 #39: 60S ribosomal protein L35-A
+分子 #40: 60S ribosomal protein L36-A
+分子 #41: 60S ribosomal protein L37-A
+分子 #42: 60S ribosomal protein L38
+分子 #43: 60S ribosomal protein L39
+分子 #44: 60S ribosomal protein L29
+分子 #45: 60S ribosomal protein L43-A
+分子 #46: 60S ribosomal protein L42-A
+分子 #47: Ribosome biogenesis protein NSA2
+分子 #48: Ribosome biogenesis protein RLP24
+分子 #49: 60S ribosomal export protein NMD3
+分子 #50: Eukaryotic translation initiation factor 6
+分子 #51: UPF0642 protein YBL028C
+分子 #52: Unknown peptide
+分子 #53: Unknown protein
+分子 #2: 35S pre-ribosomal RNA
+分子 #3: 5S rRNA
+分子 #4: 5.8S rRNA
+分子 #54: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+分子 #55: 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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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 R1.2/1.3 / メッシュ: 200 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |