+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-35413 | |||||||||
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タイトル | Dibekacin-added human 80S ribosome | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Ribosome | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / axial mesoderm development / negative regulation of formation of translation preinitiation complex / nucleolus organization / ribosomal protein import into nucleus / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / 90S preribosome assembly / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / laminin receptor activity / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein kinase A binding / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / optic nerve development / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / lung morphogenesis / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / male meiosis I / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / macrophage chemotaxis / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.59 Å | |||||||||
データ登録者 | Tomono J / Asano K / Chiashi T / Tanaka Y / Yokoyama T | |||||||||
資金援助 | 日本, 2件
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引用 | ジャーナル: J Biochem / 年: 2024 タイトル: Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. 著者: Junta Tomono / Kosuke Asano / Takuma Chiashi / Masato Suzuki / Masayuki Igarashi / Yoshiaki Takahashi / Yoshikazu Tanaka / Takeshi Yokoyama / 要旨: The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to ...The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development. | |||||||||
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_35413.map.gz | 910.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-35413-v30.xml emd-35413.xml | 102.1 KB 102.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_35413_fsc.xml | 22.6 KB | 表示 | FSCデータファイル |
画像 | emd_35413.png | 93.9 KB | ||
Filedesc metadata | emd-35413.cif.gz | 20.2 KB | ||
その他 | emd_35413_half_map_1.map.gz emd_35413_half_map_2.map.gz | 812.7 MB 812.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-35413 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35413 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_35413_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_35413_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_35413_validation.xml.gz | 29.4 KB | 表示 | |
CIF形式データ | emd_35413_validation.cif.gz | 38.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35413 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35413 | 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_35413.map.gz / 形式: CCP4 / 大きさ: 1000 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: 0.788 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
-ハーフマップ: #2
ファイル | emd_35413_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_35413_half_map_2.map | ||||||||||||
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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 : DBK-added human 80S ribosome
+超分子 #1: DBK-added human 80S ribosome
+分子 #1: 28S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #3: 5.8S ribosomal RNA
+分子 #47: 18S ribosomal RNA
+分子 #4: 60S ribosomal protein L8
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4
+分子 #7: 60S ribosomal protein L5
+分子 #8: 60S ribosomal protein L6
+分子 #9: 60S ribosomal protein L7
+分子 #10: 60S ribosomal protein L7a
+分子 #11: 60S ribosomal protein L9
+分子 #12: 60S ribosomal protein L10-like
+分子 #13: 60S ribosomal protein L11
+分子 #14: 60S ribosomal protein L13
+分子 #15: 60S ribosomal protein L14
+分子 #16: 60S ribosomal protein L15
+分子 #17: 60S ribosomal protein L13a
+分子 #18: 60S ribosomal protein L17
+分子 #19: 60S ribosomal protein L18
+分子 #20: 60S ribosomal protein L19
+分子 #21: 60S ribosomal protein L18a
+分子 #22: 60S ribosomal protein L21
+分子 #23: 60S ribosomal protein L22
+分子 #24: 60S ribosomal protein L23
+分子 #25: 60S ribosomal protein L24
+分子 #26: 60S ribosomal protein L23a
+分子 #27: 60S ribosomal protein L26
+分子 #28: 60S ribosomal protein L27
+分子 #29: 60S ribosomal protein L27a
+分子 #30: 60S ribosomal protein L29
+分子 #31: 60S ribosomal protein L30
+分子 #32: 60S ribosomal protein L31
+分子 #33: 60S ribosomal protein L32
+分子 #34: 60S ribosomal protein L35a
+分子 #35: 60S ribosomal protein L34
+分子 #36: 60S ribosomal protein L35
+分子 #37: 60S ribosomal protein L36
+分子 #38: 60S ribosomal protein L37
+分子 #39: 60S ribosomal protein L38
+分子 #40: 60S ribosomal protein L39
+分子 #41: Large ribosomal subunit protein eL40
+分子 #42: 60S ribosomal protein L41
+分子 #43: 60S ribosomal protein L36a
+分子 #44: 60S ribosomal protein L37a
+分子 #45: 60S ribosomal protein L28
+分子 #46: 60S ribosomal protein L10a
+分子 #48: 40S ribosomal protein SA
+分子 #49: 40S ribosomal protein S3a
+分子 #50: 40S ribosomal protein S3
+分子 #51: 40S ribosomal protein S4, X isoform
+分子 #52: 40S ribosomal protein S5
+分子 #53: 40S ribosomal protein S7
+分子 #54: 40S ribosomal protein S8
+分子 #55: 40S ribosomal protein S10
+分子 #56: 40S ribosomal protein S11
+分子 #57: 40S ribosomal protein S15
+分子 #58: 40S ribosomal protein S16
+分子 #59: 40S ribosomal protein S17
+分子 #60: 40S ribosomal protein S18
+分子 #61: 40S ribosomal protein S19
+分子 #62: 40S ribosomal protein S20
+分子 #63: 40S ribosomal protein S21
+分子 #64: 40S ribosomal protein S23
+分子 #65: 40S ribosomal protein S26
+分子 #66: 40S ribosomal protein S28
+分子 #67: 40S ribosomal protein S29
+分子 #68: Receptor of activated protein C kinase 1
+分子 #69: 40S ribosomal protein S2
+分子 #70: 40S ribosomal protein S6
+分子 #71: 40S ribosomal protein S9
+分子 #72: 40S ribosomal protein S12
+分子 #73: 40S ribosomal protein S13
+分子 #74: 40S ribosomal protein S14
+分子 #75: 40S ribosomal protein S15a
+分子 #76: 40S ribosomal protein S24
+分子 #77: 40S ribosomal protein S25
+分子 #78: 40S ribosomal protein S27
+分子 #79: 40S ribosomal protein S30
+分子 #80: Ubiquitin-40S ribosomal protein S27a
+分子 #81: Dibekacin
+分子 #82: MAGNESIUM ION
+分子 #83: 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 R1.2/1.3 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 10 sec. / 詳細: covered with a homemade ultra-thin carbon film |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 297 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | JEOL CRYO ARM 300 |
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特殊光学系 | エネルギーフィルター - 名称: In-column Omega Filter |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / デジタル化 - サイズ - 横: 5760 pixel / デジタル化 - サイズ - 縦: 4092 pixel / 実像数: 3682 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 20.0 µm / 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): 2.3000000000000003 µm 最小 デフォーカス(公称値): 1.1 µm / 倍率(公称値): 60000 |
試料ステージ | 試料ホルダーモデル: JEOL CRYOSPECPORTER / ホルダー冷却材: NITROGEN |