+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9530 | |||||||||
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タイトル | Cryo-EM structure of the model post-termination complex (PoTC) in the rotated state | |||||||||
マップデータ | Model post-termination complex (PoTC) in the ratcheted state | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 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 ...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 / translational termination / four-way junction DNA binding / 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / 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 / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm 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: 8.5 Å | |||||||||
データ登録者 | Iwakura N / Yokoyama T / Quaglia F / Mitsuoka K / Mio K / Shigematsu H / Shirouzu M / Kaji A / Kaji H | |||||||||
引用 | ジャーナル: PLoS One / 年: 2017 タイトル: Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G. 著者: Nobuhiro Iwakura / Takeshi Yokoyama / Fabio Quaglia / Kaoru Mitsuoka / Kazuhiro Mio / Hideki Shigematsu / Mikako Shirouzu / Akira Kaji / Hideko Kaji / 要旨: A model Post-Termination Complex (PoTC) used for the discovery of Ribosome Recycling Factor (RRF) was purified and characterized by cryo-electron microscopic analysis and biochemical methods. We ...A model Post-Termination Complex (PoTC) used for the discovery of Ribosome Recycling Factor (RRF) was purified and characterized by cryo-electron microscopic analysis and biochemical methods. We established that the model PoTC has mostly one tRNA, at the P/E or P/P position, together with one mRNA. The structural studies were supported by the biochemical measurement of bound tRNA and mRNA. Using this substrate, we establish that the release of tRNA, release of mRNA and splitting of ribosomal subunits occur during the recycling reaction. Order of these events is tRNA release first followed by mRNA release and splitting almost simultaneously. Moreover, we demonstrate that IF3 is not involved in any of the recycling reactions but simply prevents the re-association of split ribosomal subunits. Our finding demonstrates that the important function of RRF includes the release of mRNA, which is often missed by the use of a short ORF with the Shine-Dalgarno sequence near the termination site. | |||||||||
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_9530.map.gz | 95.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9530-v30.xml emd-9530.xml | 9.1 KB 9.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9530.png | 775.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9530 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9530 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9530_validation.pdf.gz | 418.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9530_full_validation.pdf.gz | 418.4 KB | 表示 | |
XML形式データ | emd_9530_validation.xml.gz | 6.3 KB | 表示 | |
CIF形式データ | emd_9530_validation.cif.gz | 7.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9530 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9530 | 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_9530.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Model post-termination complex (PoTC) in the ratcheted state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.22 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
-試料の構成要素
-全体 : Model post-termination complex (PoTC)
全体 | 名称: Model post-termination complex (PoTC) |
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要素 |
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-超分子 #1: Model post-termination complex (PoTC)
超分子 | 名称: Model post-termination complex (PoTC) / タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
-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: 7.6 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | JEOL 3100FFC |
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撮影 | フィルム・検出器のモデル: KODAK SO-163 FILM / 平均電子線量: 30.0 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 |
-画像解析
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: 8.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2) / 使用した粒子像数: 40716 |
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初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2) |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2) |