+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13805 | |||||||||
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タイトル | Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain | |||||||||
マップデータ | Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain. | |||||||||
試料 |
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キーワード | Ribosome / protein synthesis / antibiotic resistance / ARE ABC-F protein family / leader peptide / cryo-EM | |||||||||
機能・相同性 | 機能・相同性情報 transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) / Streptococcus pneumoniae (肺炎レンサ球菌) / 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: 3.0 Å | |||||||||
データ登録者 | Fostier CR / Ousalem F / Soufari H / Leroy EC / Ngo S / Innis A / Hashem Y / Boel G | |||||||||
資金援助 | フランス, 2件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Regulation of the macrolide resistance ABC-F translation factor MsrD. 著者: Corentin R Fostier / Farès Ousalem / Elodie C Leroy / Saravuth Ngo / Heddy Soufari / C Axel Innis / Yaser Hashem / Grégory Boël / 要旨: Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we ...Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_13805.map.gz | 159.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13805-v30.xml emd-13805.xml | 82.4 KB 82.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_13805.png | 93.4 KB | ||
Filedesc metadata | emd-13805.cif.gz | 52.7 KB | ||
その他 | emd_13805_additional_1.map.gz emd_13805_additional_2.map.gz emd_13805_additional_3.map.gz | 7.9 MB 1.6 MB 3.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13805 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13805 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13805_validation.pdf.gz | 650.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13805_full_validation.pdf.gz | 650.4 KB | 表示 | |
XML形式データ | emd_13805_validation.xml.gz | 7.1 KB | 表示 | |
CIF形式データ | emd_13805_validation.cif.gz | 8.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13805 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13805 | 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_13805.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 | Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain. | ||||||||||||||||||||||||||||||||||||
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: 1.15 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: 50S focused refinement (including acceptor stems of P...
ファイル | emd_13805_additional_1.map | ||||||||||||
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注釈 | 50S focused refinement (including acceptor stems of P and E tRNAs) of Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 30S-head focused refinement of Erythromycin-stalled Escherichia coli 70S...
ファイル | emd_13805_additional_2.map | ||||||||||||
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注釈 | 30S-head focused refinement of Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 30S-body focused refinement (including ASL of P and...
ファイル | emd_13805_additional_3.map | ||||||||||||
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注釈 | 30S-body focused refinement (including ASL of P and E tRNAs) of Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain. | ||||||||||||
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 : Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...
+超分子 #1: Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...
+分子 #1: 16S rRNA
+分子 #22: 23S rRNA
+分子 #23: 5S rRNA
+分子 #54: Met-tRNA (P site)
+分子 #55: Phe-tRNA (E site)
+分子 #56: MsrDL mRNA
+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 L31
+分子 #31: 50S ribosomal protein L13
+分子 #32: 50S ribosomal protein L14
+分子 #33: 50S ribosomal protein L15
+分子 #34: 50S ribosomal protein L16
+分子 #35: 50S ribosomal protein L17
+分子 #36: 50S ribosomal protein L18
+分子 #37: 50S ribosomal protein L19
+分子 #38: 50S ribosomal protein L20
+分子 #39: 50S ribosomal protein L21
+分子 #40: 50S ribosomal protein L22
+分子 #41: 50S ribosomal protein L23
+分子 #42: 50S ribosomal protein L24
+分子 #43: 50S ribosomal protein L25
+分子 #44: 50S ribosomal protein L27
+分子 #45: 50S ribosomal protein L28
+分子 #46: 50S ribosomal protein L29
+分子 #47: 50S ribosomal protein L30
+分子 #48: 50S ribosomal protein L32
+分子 #49: 50S ribosomal protein L33
+分子 #50: 50S ribosomal protein L34
+分子 #51: 50S ribosomal protein L35
+分子 #52: 50S ribosomal protein L36
+分子 #53: MsrDL: FME-TYR-LEU-ILE-PHE-MET
+分子 #57: MAGNESIUM ION
+分子 #58: ERYTHROMYCIN A
+分子 #59: water
-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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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 64.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 75000 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |