+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0139 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
キーワード | 100S / cryo-EM / E-site tRNA / hibernation / HPF / ribosome / RMF / S1 | |||||||||
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 DNA-templated DNA replication initiation / negative regulation of translational 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 / response to reactive oxygen species / transcription antitermination / translational initiation / 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 / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / single-stranded RNA binding / 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 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: 7.9 Å | |||||||||
データ登録者 | Beckert B / Turk M | |||||||||
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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_0139.map.gz | 3 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-0139-v30.xml emd-0139.xml | 72 KB 72 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0139_fsc.xml | 8.2 KB | 表示 | FSCデータファイル |
画像 | emd_0139.png | 174 KB | ||
Filedesc metadata | emd-0139.cif.gz | 13.6 KB | ||
その他 | emd_0139_additional_1.map.gz emd_0139_additional_2.map.gz | 286.9 MB 286.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0139 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0139 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0139_validation.pdf.gz | 423 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_0139_full_validation.pdf.gz | 422.5 KB | 表示 | |
XML形式データ | emd_0139_validation.xml.gz | 10.5 KB | 表示 | |
CIF形式データ | emd_0139_validation.cif.gz | 13.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0139 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0139 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_0139.map.gz / 形式: CCP4 / 大きさ: 45.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: #1
ファイル | emd_0139_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: #2
ファイル | emd_0139_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
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: 50S ribosomal protein L32
+分子 #2: 50S ribosomal protein L33
+分子 #3: 50S ribosomal protein L34
+分子 #4: 50S ribosomal protein L35
+分子 #5: 50S ribosomal protein L36
+分子 #6: 50S ribosomal protein L31
+分子 #9: 50S ribosomal protein L2
+分子 #10: 50S ribosomal protein L3
+分子 #11: 50S ribosomal protein L4
+分子 #12: 50S ribosomal protein L5
+分子 #13: 50S ribosomal protein L6
+分子 #14: 50S ribosomal protein L9
+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 #33: 30S ribosomal protein S2
+分子 #34: 30S ribosomal protein S3
+分子 #35: 30S ribosomal protein S4
+分子 #36: 30S ribosomal protein S5
+分子 #37: 30S ribosomal protein S6
+分子 #38: 30S ribosomal protein S7
+分子 #39: 30S ribosomal protein S8
+分子 #40: 30S ribosomal protein S9
+分子 #41: 30S ribosomal protein S10
+分子 #42: 30S ribosomal protein S11
+分子 #43: 30S ribosomal protein S12
+分子 #44: 30S ribosomal protein S13
+分子 #45: 30S ribosomal protein S14
+分子 #46: 30S ribosomal protein S15
+分子 #47: 30S ribosomal protein S16
+分子 #48: 30S ribosomal protein S17
+分子 #49: 30S ribosomal protein S18
+分子 #50: 30S ribosomal protein S19
+分子 #51: 30S ribosomal protein S20
+分子 #52: 30S ribosomal protein S21
+分子 #53: Ribosome modulation factor
+分子 #54: Ribosome hibernation promoting factor
+分子 #55: 30S ribosomal protein S1
+分子 #7: 23S ribosomal RNA
+分子 #8: 5S ribosomal RNA
+分子 #32: 16S ribosomal RNA
+分子 #56: tRNA Mixture
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. |
凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 1.15 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 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |