+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3730 | |||||||||
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タイトル | Cryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome | |||||||||
マップデータ | Cryo-EM reconstruction of an E. coli 70S ribosome in complex with Api137 and RF1. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / 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 ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / 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 / four-way junction DNA binding / translational termination / 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 / 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 (strain K12) (大腸菌) / Staphylococcus aureus (黄色ブドウ球菌) / Apis mellifera (セイヨウミツバチ) / Escherichia coli K-12 (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: 3.4 Å | |||||||||
データ登録者 | Graf M / Berninghausen O / Beckmann R / Wilson DN | |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2017 タイトル: An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome. 著者: Tanja Florin / Cristina Maracci / Michael Graf / Prajwal Karki / Dorota Klepacki / Otto Berninghausen / Roland Beckmann / Nora Vázquez-Laslop / Daniel N Wilson / Marina V Rodnina / Alexander S Mankin / 要旨: Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a ...Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factor (RF) RF1 or RF2 subsequent to the release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with RF1 and Api137 reveals the molecular interactions that lead to RF trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons before polypeptide release, thereby resulting in a global shutdown of translation termination. | |||||||||
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_3730.map.gz | 21.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3730-v30.xml emd-3730.xml | 74.2 KB 74.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3730.png | 147.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3730 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3730_validation.pdf.gz | 261 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3730_full_validation.pdf.gz | 260.1 KB | 表示 | |
XML形式データ | emd_3730_validation.xml.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3730 | 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_3730.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM reconstruction of an E. coli 70S ribosome in complex with Api137 and RF1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.084 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
-試料の構成要素
+全体 : Escherichia coli 70S ribosome
+超分子 #1: Escherichia coli 70S ribosome
+超分子 #2: Escherichia coli 70S ribosome
+超分子 #3: mRNA
+超分子 #4: Apidaecin
+分子 #1: 23S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #34: mRNA
+分子 #35: 16S ribosomal RNA
+分子 #57: P-site Ile-tRNA
+分子 #3: 50S ribosomal protein L2
+分子 #4: 50S ribosomal protein L3
+分子 #5: 50S ribosomal protein L4
+分子 #6: 50S ribosomal protein L5
+分子 #7: 50S ribosomal protein L6
+分子 #8: 50S ribosomal protein L9
+分子 #9: 50S ribosomal protein L11
+分子 #10: 50S ribosomal protein L13
+分子 #11: 50S ribosomal protein L14
+分子 #12: 50S ribosomal protein L15
+分子 #13: 50S ribosomal protein L16
+分子 #14: 50S ribosomal protein L17
+分子 #15: 50S ribosomal protein L18
+分子 #16: 50S ribosomal protein L19
+分子 #17: 50S ribosomal protein L20
+分子 #18: 50S ribosomal protein L21
+分子 #19: 50S ribosomal protein L22
+分子 #20: 50S ribosomal protein L23
+分子 #21: 50S ribosomal protein L24
+分子 #22: 50S ribosomal protein L25
+分子 #23: 50S ribosomal protein L27
+分子 #24: 50S ribosomal protein L28
+分子 #25: 50S ribosomal protein L29
+分子 #26: 50S ribosomal protein L30
+分子 #27: 50S ribosomal protein L32
+分子 #28: 50S ribosomal protein L33
+分子 #29: 50S ribosomal protein L34
+分子 #30: 50S ribosomal protein L35
+分子 #31: 50S ribosomal protein L36
+分子 #32: 50S ribosomal protein L10
+分子 #33: 50S ribosomal protein L31
+分子 #36: 30S ribosomal protein S2
+分子 #37: 30S ribosomal protein S3
+分子 #38: 30S ribosomal protein S4
+分子 #39: 30S ribosomal protein S5
+分子 #40: 30S ribosomal protein S6
+分子 #41: 30S ribosomal protein S7
+分子 #42: 30S ribosomal protein S8
+分子 #43: 30S ribosomal protein S9
+分子 #44: 30S ribosomal protein S10
+分子 #45: 30S ribosomal protein S11
+分子 #46: 30S ribosomal protein S12
+分子 #47: 30S ribosomal protein S13
+分子 #48: 30S ribosomal protein S14
+分子 #49: 30S ribosomal protein S15
+分子 #50: 30S ribosomal protein S16
+分子 #51: 30S ribosomal protein S17
+分子 #52: 30S ribosomal protein S18
+分子 #53: 30S ribosomal protein S19
+分子 #54: 30S ribosomal protein S20
+分子 #55: 30S ribosomal protein S21
+分子 #56: Peptide chain release factor RF1
+分子 #58: Apidaecin
-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: 7.4 |
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グリッド | モデル: Quantifoil R3/3 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-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) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 撮影したグリッド数: 1 / 実像数: 5132 / 平均電子線量: 28.0 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 |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-5o2r: |