+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0662 | |||||||||||||||
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タイトル | 70S initiation complex | |||||||||||||||
マップデータ | 70S initiation complex with IF2 and P/I tRNA | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity ...guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / 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 / chaperone-mediated protein folding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translation initiation factor activity / response to cold / 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 / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR 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 / ribonucleoprotein complex / 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) / Escherichia coli | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||||||||
データ登録者 | Frank J / Gonzalez Jr RL / kaledhonkar S / Fu Z / Caban K / Li W / Chen B / Sun M | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. 著者: Sandip Kaledhonkar / Ziao Fu / Kelvin Caban / Wen Li / Bo Chen / Ming Sun / Ruben L Gonzalez / Joachim Frank / 要旨: The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to ...The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation. Although comparisons of the structures of the 30S and 70S initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNA can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNA that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNA positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology. | |||||||||||||||
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_0662.map.gz | 6.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0662-v30.xml emd-0662.xml | 60.7 KB 60.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0662_fsc.xml | 9.1 KB | 表示 | FSCデータファイル |
画像 | emd_0662.png | 233.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0662 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0662 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0662_validation.pdf.gz | 404.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0662_full_validation.pdf.gz | 404 KB | 表示 | |
XML形式データ | emd_0662_validation.xml.gz | 10.9 KB | 表示 | |
CIF形式データ | emd_0662_validation.cif.gz | 14.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0662 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0662 | 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_0662.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 70S initiation complex with IF2 and P/I tRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.66 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 : 70S elongation competent ribosome
+超分子 #1: 70S elongation competent ribosome
+分子 #1: 16S rRNA
+分子 #22: mRNA
+分子 #23: tRNA
+分子 #25: 23S rRNA
+分子 #44: 5S rRNA
+分子 #2: 30S ribosomal protein S2
+分子 #3: 30S ribosomal protein S3
+分子 #4: 30S ribosomal protein S4
+分子 #5: 30S ribosomal protein S5
+分子 #6: 30S ribosomal protein S6
+分子 #7: 30S ribosomal protein S7
+分子 #8: 30S ribosomal protein S8
+分子 #9: 30S ribosomal protein S9
+分子 #10: 30S ribosomal protein S10
+分子 #11: 30S ribosomal protein S11
+分子 #12: 30S ribosomal protein S12
+分子 #13: 30S ribosomal protein S13
+分子 #14: 30S ribosomal protein S14
+分子 #15: 30S ribosomal protein S15
+分子 #16: 30S ribosomal protein S16
+分子 #17: 30S ribosomal protein S17
+分子 #18: 30S ribosomal protein S18
+分子 #19: 30S ribosomal protein S19
+分子 #20: 30S ribosomal protein S20
+分子 #21: 30S ribosomal protein S21
+分子 #24: Translation initiation factor IF-2
+分子 #26: 50S ribosomal protein L4
+分子 #27: 50S ribosomal protein L5
+分子 #28: 50S ribosomal protein L10
+分子 #29: 50S ribosomal protein L6
+分子 #30: 50S ribosomal protein L11
+分子 #31: 50S ribosomal protein L13
+分子 #32: 50S ribosomal protein L14
+分子 #33: 50S ribosomal protein L15
+分子 #34: 50S ribosomal protein L16
+分子 #35: 50S ribosomal protein L17
+分子 #36: 50S ribosomal protein L18
+分子 #37: 50S ribosomal protein L19
+分子 #38: 50S ribosomal protein L20
+分子 #39: 50S ribosomal protein L21
+分子 #40: 50S ribosomal protein L22
+分子 #41: 50S ribosomal protein L23
+分子 #42: 50S ribosomal protein L24
+分子 #43: 50S ribosomal protein L25
+分子 #45: 50S ribosomal protein L36
+分子 #46: 50S ribosomal protein L27
+分子 #47: 50S ribosomal protein L28
+分子 #48: 50S ribosomal protein L29
+分子 #49: 50S ribosomal protein L30
+分子 #50: 50S ribosomal protein L3
+分子 #51: 50S ribosomal protein L32
+分子 #52: 50S ribosomal protein L33
+分子 #53: 50S ribosomal protein L34
+分子 #54: 50S ribosomal protein L35
+分子 #55: 50S ribosomal protein L2
-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 | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F30 |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 35.0 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: OTHER / 撮影モード: DARK FIELD |
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 34096 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
FSC曲線 (解像度の算出) |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-6o9k: |