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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 | Damaged 70S ribosome with PrfH bound | |||||||||
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機能・相同性 | ![]() translation release factor activity / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit ...translation release factor activity / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / membrane / 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: 2.55 Å | |||||||||
![]() | Tian Y / Zeng F / Raybarman A / Carruthers A / Li Q / Fatma S / Huang RH | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB. 著者: Yannan Tian / Fuxing Zeng / Adrika Raybarman / Shirin Fatma / Amy Carruthers / Qingrong Li / Raven H Huang / ![]() ![]() 要旨: RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of ...RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-Å cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3'-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2-PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival. | |||||||||
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 | ![]() | 202.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 73.5 KB 73.5 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.5 KB | 表示 | ![]() |
画像 | ![]() | 134.5 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 576.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 575.9 KB | 表示 | |
XML形式データ | ![]() | 13.2 KB | 表示 | |
CIF形式データ | ![]() | 18 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 | ![]() 7sa4MC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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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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ボクセルのサイズ | X=Y=Z: 1.05 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
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試料の構成要素
+全体 : Damaged 70S with PrfH
+超分子 #1: Damaged 70S with PrfH
+超分子 #2: 50S
+超分子 #3: 30S
+超分子 #4: tRNA
+超分子 #5: Putative peptide chain release factor homolog
+分子 #1: 23S ribosomal RNA
+分子 #2: 16S ribosomal RNA
+分子 #3: 5S ribosomal RNA
+分子 #4: P-tRNA, E-tRNA
+分子 #5: mRNA
+分子 #6: Peptide chain release factor H
+分子 #7: 50S ribosomal protein L2
+分子 #8: 50S ribosomal protein L3
+分子 #9: 50S ribosomal protein L4
+分子 #10: 50S ribosomal protein L5
+分子 #11: 50S ribosomal protein L6
+分子 #12: 50S ribosomal protein L9
+分子 #13: 50S ribosomal protein L10
+分子 #14: 50S ribosomal protein L11
+分子 #15: 50S ribosomal protein L13
+分子 #16: 50S ribosomal protein L14
+分子 #17: 50S ribosomal protein L15
+分子 #18: 50S ribosomal protein L16
+分子 #19: 50S ribosomal protein L17
+分子 #20: 50S ribosomal protein L18
+分子 #21: 50S ribosomal protein L19
+分子 #22: 50S ribosomal protein L20
+分子 #23: 50S ribosomal protein L21
+分子 #24: 50S ribosomal protein L22
+分子 #25: 50S ribosomal protein L23
+分子 #26: 50S ribosomal protein L24
+分子 #27: 50S ribosomal protein L25
+分子 #28: 50S ribosomal protein L27
+分子 #29: 50S ribosomal protein L28
+分子 #30: 50S ribosomal protein L29
+分子 #31: 50S ribosomal protein L30
+分子 #32: 50S ribosomal protein L31
+分子 #33: 50S ribosomal protein L32
+分子 #34: 50S ribosomal protein L33
+分子 #35: 50S ribosomal protein L34
+分子 #36: 50S ribosomal protein L35
+分子 #37: 50S ribosomal protein L36
+分子 #38: 30S ribosomal protein S2
+分子 #39: 30S ribosomal protein S3
+分子 #40: 30S ribosomal protein S4
+分子 #41: 30S ribosomal protein S5
+分子 #42: 30S ribosomal protein S6
+分子 #43: 30S ribosomal protein S7
+分子 #44: 30S ribosomal protein S8
+分子 #45: 30S ribosomal protein S9
+分子 #46: 30S ribosomal protein S10
+分子 #47: 30S ribosomal protein S11
+分子 #48: 30S ribosomal protein S12
+分子 #49: 30S ribosomal protein S13
+分子 #50: 30S ribosomal protein S14
+分子 #51: 30S ribosomal protein S15
+分子 #52: 30S ribosomal protein S16
+分子 #53: 30S ribosomal protein S17
+分子 #54: 30S ribosomal protein S18
+分子 #55: 30S ribosomal protein S19
+分子 #56: 30S ribosomal protein S20
+分子 #57: 30S ribosomal protein S21
+分子 #58: MAGNESIUM ION
+分子 #59: ZINC ION
+分子 #60: water
-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: 7.4 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 / 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: 0.4 nm / 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: FEI FALCON III (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 30.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |