+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6311 | |||||||||
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タイトル | Cryo-EM structure of tetracycline resistance protein TetM bound to a translating E. coli ribosome | |||||||||
マップデータ | Reconstruction of TetM bound to translating E. coli ribosomes. | |||||||||
試料 |
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キーワード | antibiotics (抗生物質) / protein synthesis (タンパク質生合成) / resistance / ribosome (リボソーム) / TetM / tetracycline (テトラサイクリン) / tigecycline / translation (翻訳 (生物学)) | |||||||||
機能・相同性 | 機能・相同性情報 ribosome disassembly / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...ribosome disassembly / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / 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 translational initiation / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / cytosolic ribosome assembly / DNA endonuclease activity / regulation of DNA-templated transcription elongation / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / リボソーム生合成 / ribosome binding / regulation of translation / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / 生体膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) / Enterococcus faecalis (乳酸球菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Arenz S / Nguyen F / Beckmann R / Wilson DN | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9-Å resolution. 著者: Stefan Arenz / Fabian Nguyen / Roland Beckmann / Daniel N Wilson / 要旨: Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16- ...Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16-Å resolution structures of RPPs bound to vacant or nontranslating ribosomes. Here we present a cryo-electron microscopy reconstruction of the RPP TetM in complex with a translating ribosome at 3.9-Å resolution. The structure reveals the contacts of TetM with the ribosome, including interaction between the conserved and functionally critical C-terminal extension of TetM with a unique splayed conformation of nucleotides A1492 and A1493 at the decoding center of the small subunit. The resolution enables us to unambiguously model the side chains of the amino acid residues comprising loop III in domain IV of TetM, revealing that the tyrosine residues Y506 and Y507 are not responsible for drug-release as suggested previously but rather for intrafactor contacts that appear to stabilize the conformation of loop III. Instead, Pro509 at the tip of loop III is located directly within the tetracycline binding site where it interacts with nucleotide C1054 of the 16S rRNA, such that RPP action uses Pro509, rather than Y506/Y507, to directly dislodge and release tetracycline from the ribosome. | |||||||||
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_6311.map.gz | 175.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6311-v30.xml emd-6311.xml | 9.8 KB 9.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6311.png | 111.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6311 | 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_6311.map.gz / 形式: CCP4 / 大きさ: 185.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of TetM bound to translating E. coli ribosomes. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : TetM bound to ErmCL-RNCs
全体 | 名称: TetM bound to ErmCL-RNCs |
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要素 |
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-超分子 #1000: TetM bound to ErmCL-RNCs
超分子 | 名称: TetM bound to ErmCL-RNCs / タイプ: sample / ID: 1000 / Number unique components: 2 |
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-超分子 #1: ErmCL-stalled ribosome
超分子 | 名称: ErmCL-stalled ribosome / タイプ: complex / ID: 1 / 組換発現: No / データベース: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
-分子 #1: Tetracycline resistance protein TetM
分子 | 名称: Tetracycline resistance protein TetM / タイプ: protein_or_peptide / ID: 1 / Name.synonym: TetM / コピー数: 1 / 集合状態: monomer / 組換発現: Yes |
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由来(天然) | 生物種: Enterococcus faecalis (乳酸球菌) |
組換発現 | 生物種: Escherichia coli BL21 (大腸菌) |
-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 詳細: 50 mM HEPES-KOH, 100 mM KOAc, 25 mM Mg(OAc)2, 6 mM b-mercaptoethanol |
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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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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 FIELDBright-field microscopy / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.7 µm / 倍率(公称値): 125085 / Cs: mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
Cs | 0 |
日付 | 2014年3月14日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 2753 / 平均電子線量: 28 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Defocus groups |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: SPIDER 詳細: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, an FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A ...詳細: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, an FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). The final map was sharpened by applying an automatically determined negative B-factor using the program EMBFACTOR (Fernandez et al, 2008). 使用した粒子像数: 78186 |