+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10353 | |||||||||
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タイトル | Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Cryo-EM / bacterial ribosome rescue / Bacillus ribosome rescue factor A / Bacillus subtilis peptide chain release factor 2 / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 translation release factor activity, codon specific / 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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...translation release factor activity, codon specific / 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 / 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 / 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 K-12 (大腸菌) / Bacillus subtilis (strain 168) (枯草菌) / Escherichia coli (strain K12) (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: 3.06 Å | |||||||||
データ登録者 | Muller C / Beckert B | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Commun / 年: 2019 タイトル: Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. 著者: Naomi Shimokawa-Chiba / Claudia Müller / Keigo Fujiwara / Bertrand Beckert / Koreaki Ito / Daniel N Wilson / Shinobu Chiba / 要旨: Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some ...Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. | |||||||||
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_10353.map.gz | 20 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10353-v30.xml emd-10353.xml | 85.5 KB 85.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10353_fsc.xml | 13.1 KB | 表示 | FSCデータファイル |
画像 | emd_10353.png | 40.2 KB | ||
Filedesc metadata | emd-10353.cif.gz | 14.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10353 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10353_validation.pdf.gz | 289 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10353_full_validation.pdf.gz | 288.1 KB | 表示 | |
XML形式データ | emd_10353_validation.xml.gz | 13.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10353 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10353 | 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_10353.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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ボクセルのサイズ | X=Y=Z: 1.065 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 : E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
+超分子 #1: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
+超分子 #2: Escherichia coli ribosome with P-site tRNA-Pro(CGG, carrying the ...
+超分子 #3: Bacillus subtilis ribosome rescue factor (BrfA; former YqkK) and ...
+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 #55: Uncharacterized protein YqkK
+分子 #56: Peptide chain release factor 2
+分子 #7: 23S ribosomal RNA
+分子 #8: 5S ribosomal RNA
+分子 #32: 16S ribosomal RNA
+分子 #53: mRNA
+分子 #54: P-site tRNA-Pro(CGG)
-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: 7.2 |
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凍結 | 凍結剤: ETHANE |
-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 III (4k x 4k) 平均電子線量: 83.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |