+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0080 | |||||||||||||||
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タイトル | Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II) | |||||||||||||||
マップデータ | Cryo-EM map of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II) | |||||||||||||||
試料 |
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キーワード | single particle cryo-EM / GTPase / ribosome / release factor RF1 / RF2 / RF3 / subunit rotation / translation termination | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / GDP binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / 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 / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||||||||
生物種 | Escherichia coli (大腸菌) | |||||||||||||||
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 | Graf M / Huter P | |||||||||||||||
資金援助 | ドイツ, チェコ, 4件
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引用 | ジャーナル: Nat Commun / 年: 2018 タイトル: Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1. 著者: Michael Graf / Paul Huter / Cristina Maracci / Miroslav Peterek / Marina V Rodnina / Daniel N Wilson / 要旨: During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ...During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the Apidaecin 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome. | |||||||||||||||
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_0080.map.gz | 86.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0080-v30.xml emd-0080.xml | 72.5 KB 72.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0080.png | 86.6 KB | ||
Filedesc metadata | emd-0080.cif.gz | 14.2 KB | ||
その他 | emd_0080_additional.map.gz | 165.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0080 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0080 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0080_validation.pdf.gz | 303.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0080_full_validation.pdf.gz | 303.1 KB | 表示 | |
XML形式データ | emd_0080_validation.xml.gz | 6.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0080 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0080 | 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_0080.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM map of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.061 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
-追加マップ: Locally filtered cryo-EM map of an E. coli...
ファイル | emd_0080_additional.map | ||||||||||||
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注釈 | Locally filtered cryo-EM map of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II) | ||||||||||||
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 : In-vitro reconstitution of E. coli 70S ribosomes with RF3-GDPCP, ...
+超分子 #1: In-vitro reconstitution of E. coli 70S ribosomes with RF3-GDPCP, ...
+分子 #1: 23S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #33: mRNA
+分子 #34: 16S ribosomal RNA
+分子 #57: fMet-tRNA
+分子 #3: 50S ribosomal protein L2
+分子 #4: 50S ribosomal protein L3
+分子 #5: 50S ribosomal protein L4
+分子 #6: 50S ribosomal protein L5
+分子 #7: 50S ribosomal protein L6
+分子 #8: 50S ribosomal protein L9
+分子 #9: 50S ribosomal protein L11
+分子 #10: 50S ribosomal protein L13
+分子 #11: 50S ribosomal protein L14
+分子 #12: 50S ribosomal protein L15
+分子 #13: 50S ribosomal protein L16
+分子 #14: 50S ribosomal protein L17
+分子 #15: 50S ribosomal protein L18
+分子 #16: 50S ribosomal protein L19
+分子 #17: 50S ribosomal protein L20
+分子 #18: 50S ribosomal protein L21
+分子 #19: 50S ribosomal protein L22
+分子 #20: 50S ribosomal protein L23
+分子 #21: 50S ribosomal protein L24
+分子 #22: 50S ribosomal protein L25
+分子 #23: 50S ribosomal protein L27
+分子 #24: 50S ribosomal protein L28
+分子 #25: 50S ribosomal protein L29
+分子 #26: 50S ribosomal protein L30
+分子 #27: 50S ribosomal protein L32
+分子 #28: 50S ribosomal protein L33
+分子 #29: 50S ribosomal protein L34
+分子 #30: 50S ribosomal protein L35
+分子 #31: 50S ribosomal protein L36
+分子 #32: 50S ribosomal protein L10
+分子 #35: 30S ribosomal protein S2
+分子 #36: 30S ribosomal protein S3
+分子 #37: 30S ribosomal protein S4
+分子 #38: 30S ribosomal protein S5
+分子 #39: 30S ribosomal protein S6
+分子 #40: 30S ribosomal protein S7
+分子 #41: 30S ribosomal protein S8
+分子 #42: 30S ribosomal protein S9
+分子 #43: 30S ribosomal protein S10
+分子 #44: 30S ribosomal protein S11
+分子 #45: 30S ribosomal protein S12
+分子 #46: 30S ribosomal protein S13
+分子 #47: 30S ribosomal protein S14
+分子 #48: 30S ribosomal protein S15
+分子 #49: 30S ribosomal protein S16
+分子 #50: 30S ribosomal protein S17
+分子 #51: 30S ribosomal protein S18
+分子 #52: 30S ribosomal protein S19
+分子 #53: 30S ribosomal protein S20
+分子 #54: 30S ribosomal protein S21
+分子 #55: Peptide chain release factor RF1
+分子 #56: Peptide chain release factor RF3
+分子 #58: Apidaecin
+分子 #59: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-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: 7.4 構成要素:
詳細: Solutions were preapred fresh and filtered previous to usage. | |||||||||||||||
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凍結 | 凍結剤: ETHANE / 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 / 平均電子線量: 45.9 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 49415 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | PDB-6gxm: |