+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8237 | |||||||||||||||||||||
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タイトル | Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution | |||||||||||||||||||||
マップデータ | Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution | |||||||||||||||||||||
試料 |
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キーワード | Avilamycin / evernimycin / antibiotic / antimicrobial / ribosome / cryo-EM / smFRET / rRNA / L16 / resistance / translation | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / translational termination / 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 / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / 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 (大腸菌) / Escherichia coli (strain K12) (大腸菌) / Synthetic (人工物) | |||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||||||||||||||
データ登録者 | Arenz S / Juette MF | |||||||||||||||||||||
資金援助 | 米国, ドイツ, 6件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2016 タイトル: Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. 著者: Stefan Arenz / Manuel F Juette / Michael Graf / Fabian Nguyen / Paul Huter / Yury S Polikanov / Scott C Blanchard / Daniel N Wilson / 要旨: The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics ...The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis. | |||||||||||||||||||||
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_8237.map.gz | 157.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8237-v30.xml emd-8237.xml | 72.7 KB 72.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8237.png | 234 KB | ||
Filedesc metadata | emd-8237.cif.gz | 14.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8237 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8237 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8237_validation.pdf.gz | 662.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8237_full_validation.pdf.gz | 662.3 KB | 表示 | |
XML形式データ | emd_8237_validation.xml.gz | 6.8 KB | 表示 | |
CIF形式データ | emd_8237_validation.cif.gz | 7.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8237 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8237 | 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_8237.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 | Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.108 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 : Cryo-EM structure of the Escherichia coli 70S ribosome in complex...
+超分子 #1: Cryo-EM structure of the Escherichia coli 70S ribosome in complex...
+分子 #1: 23S Ribosomal RNA
+分子 #2: 5S Ribosomal RNA
+分子 #33: 16S Ribosomal RNA
+分子 #54: mRNA
+分子 #55: P-site 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 L10
+分子 #10: 50S ribosomal protein L11
+分子 #11: 50S ribosomal protein L13
+分子 #12: 50S ribosomal protein L14
+分子 #13: 50S ribosomal protein L15
+分子 #14: 50S ribosomal protein L16
+分子 #15: 50S ribosomal protein L17
+分子 #16: 50S ribosomal protein L18
+分子 #17: 50S ribosomal protein L19
+分子 #18: 50S ribosomal protein L20
+分子 #19: 50S ribosomal protein L21
+分子 #20: 50S ribosomal protein L22
+分子 #21: 50S ribosomal protein L23
+分子 #22: 50S ribosomal protein L24
+分子 #23: 50S ribosomal protein L25
+分子 #24: 50S ribosomal protein L27
+分子 #25: 50S ribosomal protein L28
+分子 #26: 50S ribosomal protein L29
+分子 #27: 50S ribosomal protein L30
+分子 #28: 50S ribosomal protein L32
+分子 #29: 50S ribosomal protein L33
+分子 #30: 50S ribosomal protein L34
+分子 #31: 50S ribosomal protein L35
+分子 #32: 50S ribosomal protein L36
+分子 #34: 30S ribosomal protein S2
+分子 #35: 30S ribosomal protein S3
+分子 #36: 30S ribosomal protein S4
+分子 #37: 30S ribosomal protein S5
+分子 #38: 30S ribosomal protein S6
+分子 #39: 30S ribosomal protein S7
+分子 #40: 30S ribosomal protein S8
+分子 #41: 30S ribosomal protein S9
+分子 #42: 30S ribosomal protein S10
+分子 #43: 30S ribosomal protein S11
+分子 #44: 30S ribosomal protein S12
+分子 #45: 30S ribosomal protein S13
+分子 #46: 30S ribosomal protein S14
+分子 #47: 30S ribosomal protein S15
+分子 #48: 30S ribosomal protein S16
+分子 #49: 30S ribosomal protein S17
+分子 #50: 30S ribosomal protein S18
+分子 #51: 30S ribosomal protein S19
+分子 #52: 30S ribosomal protein S20
+分子 #53: 30S ribosomal protein S21
+分子 #56: (2R,3S,4R,6S)-4-hydroxy-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7aR)-4'-hyd...
+分子 #57: ZINC ION
-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 / 材質: COPPER / 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 |
-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 / デジタル化 - 画像ごとのフレーム数: 1-4 / 平均電子線量: 20.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最大 デフォーカス(補正後): 2.4 µm / 最小 デフォーカス(補正後): 0.8 µm / 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 |
+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 / 当てはまり具合の基準: Correlation coefficient |
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得られたモデル | PDB-5kcr: |