+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0137 | |||||||||
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タイトル | Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome | |||||||||
マップデータ | None | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / 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 / 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 / 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 / single-stranded RNA binding / rRNA binding / negative regulation of translation / 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 / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli BW25113 (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: 3.0 Å | |||||||||
データ登録者 | Beckert B / Turk M / Czech A / Berninghausen O / Beckmann R / Ignatova Z / Plitzko J / Wilson ND | |||||||||
引用 | ジャーナル: Nat Microbiol / 年: 2018 タイトル: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. 著者: Bertrand Beckert / Martin Turk / Andreas Czech / Otto Berninghausen / Roland Beckmann / Zoya Ignatova / Jürgen M Plitzko / Daniel N Wilson / 要旨: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S ...To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation. | |||||||||
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_0137.map.gz | 16 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0137-v30.xml emd-0137.xml | 68.3 KB 68.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0137_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_0137.png | 238.3 KB | ||
その他 | emd_0137_additional_1.map.gz emd_0137_additional_2.map.gz | 149.1 MB 149.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0137 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0137 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0137_validation.pdf.gz | 282.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0137_full_validation.pdf.gz | 281.9 KB | 表示 | |
XML形式データ | emd_0137_validation.xml.gz | 12.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0137 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0137 | 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_0137.map.gz / 形式: CCP4 / 大きさ: 190.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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: half map
ファイル | emd_0137_additional_1.map | ||||||||||||
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注釈 | half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: half map
ファイル | emd_0137_additional_2.map | ||||||||||||
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注釈 | half map | ||||||||||||
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 : Structure of a hibernating 100S ribosome reveals an inactive conf...
+超分子 #1: Structure of a hibernating 100S ribosome reveals an inactive conf...
+分子 #1: 16S ribosomal RNA
+分子 #22: 23S ribosomal RNA
+分子 #23: 5S ribosomal RNA
+分子 #53: tRNA
+分子 #57: RNA (5'-R(P*CP*UP*CP*CP*U)-3')
+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: 50S ribosomal protein L2
+分子 #25: 50S ribosomal protein L3
+分子 #26: 50S ribosomal protein L4
+分子 #27: 50S ribosomal protein L5
+分子 #28: 50S ribosomal protein L6
+分子 #29: 50S ribosomal protein L9
+分子 #30: 50S ribosomal protein L13
+分子 #31: 50S ribosomal protein L14
+分子 #32: 50S ribosomal protein L15
+分子 #33: 50S ribosomal protein L16
+分子 #34: 50S ribosomal protein L17
+分子 #35: 50S ribosomal protein L18
+分子 #36: 50S ribosomal protein L19
+分子 #37: 50S ribosomal protein L20
+分子 #38: 50S ribosomal protein L21
+分子 #39: 50S ribosomal protein L22
+分子 #40: 50S ribosomal protein L23
+分子 #41: 50S ribosomal protein L24
+分子 #42: 50S ribosomal protein L25
+分子 #43: 50S ribosomal protein L27
+分子 #44: 50S ribosomal protein L28
+分子 #45: 50S ribosomal protein L29
+分子 #46: 50S ribosomal protein L30
+分子 #47: 50S ribosomal protein L32
+分子 #48: 50S ribosomal protein L33
+分子 #49: 50S ribosomal protein L34
+分子 #50: 50S ribosomal protein L35
+分子 #51: 50S ribosomal protein L36
+分子 #52: 50S ribosomal protein L31
+分子 #54: Ribosome modulation factor
+分子 #55: 30S ribosomal protein S1
+分子 #56: Ribosome hibernation promoting factor
-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 詳細: B100S buffer (25 mM Hepes pH 7.5, 100 mM KOAc, 15 mM Mg(OAc)2, 1 mM dithiothreitol) |
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グリッド | モデル: Quantifoil, UltrAuFoil, R1.2/1.3 / 材質: GOLD |
凍結 | 凍結剤: ETHANE-PROPANE / 装置: FEI VITROBOT MARK III |
-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) 平均電子線量: 2.5 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
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6h4n: |