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データを開く
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基本情報
| 登録情報 | ![]() | ||||||||||||
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| タイトル | Cryo-EM map of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) shows strong density for the A site tRNA | ||||||||||||
マップデータ | Cryo-EM map of the Candida albicans ribosome in complex with mRNA and initiator tRNA (strong A site tRNA), and two compounds. | ||||||||||||
試料 |
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キーワード | Candida albicans / ribosome / mRNA / mefloquine / geneticin G418 | ||||||||||||
| 機能・相同性 | 機能・相同性情報filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / filamentous growth of a population of unicellular organisms in response to starvation / filamentous growth of a population of unicellular organisms in response to biotic stimulus / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / invasive growth in response to glucose limitation / GCN2-mediated signaling ...filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / filamentous growth of a population of unicellular organisms in response to starvation / filamentous growth of a population of unicellular organisms in response to biotic stimulus / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / invasive growth in response to glucose limitation / GCN2-mediated signaling / hyphal cell wall / negative regulation of p38MAPK cascade / ribosome hibernation / preribosome / filamentous growth / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / preribosome, small subunit precursor / mRNA destabilization / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / negative regulation of translational frameshifting / signaling receptor activator activity / translational elongation / G-protein alpha-subunit binding / 90S preribosome / ribosomal subunit export from nucleus / protein-RNA complex assembly / protein-membrane adaptor activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of autophagy / rescue of stalled cytosolic ribosome / protein kinase C binding / cellular response to starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / extracellular vesicle / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / cell adhesion / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / cell surface / RNA binding / extracellular region / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
| 生物種 | Candida albicans SC5314 (酵母) / Candida albicans (酵母) | ||||||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.35 Å | ||||||||||||
データ登録者 | Kolosova O / Zgadzay Y / Jenner LB / Guskov A / Yusupov M | ||||||||||||
| 資金援助 | フランス, 3件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2025タイトル: Mechanism of read-through enhancement by aminoglycosides and mefloquine. 著者: Olga Kolosova / Yury Zgadzay / Artem Stetsenko / Anastasia P Sukhinina / Anastasia Atamas / Shamil Validov / Andrey Rogachev / Konstantin Usachev / Lasse Jenner / Sergey E Dmitriev / Gulnara ...著者: Olga Kolosova / Yury Zgadzay / Artem Stetsenko / Anastasia P Sukhinina / Anastasia Atamas / Shamil Validov / Andrey Rogachev / Konstantin Usachev / Lasse Jenner / Sergey E Dmitriev / Gulnara Yusupova / Albert Guskov / Marat Yusupov / ![]() 要旨: Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of ...Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of aminoglycosides, particularly in combination with stop-codon read-through enhancers, for developing drugs that can rescue the production of full-length proteins. Using X-ray crystallography and single-particle cryo-EM, we obtained structures of the eukaryotic ribosome in complexes with several aminoglycosides (geneticin G418, paromomycin, and hygromycin B) and the antimalarial drug mefloquine (MFQ), which has also been identified as a read-through enhancer. Our study reveals a binding site of MFQ, which holds significant promise for the development of therapies targeting premature termination codon-related genetic and oncological diseases. The results underscore the crucial role of the bridge B7b/c in mediating the effects of MFQ on subunit rotation dynamics. Through a comprehensive analysis of the interactions between the drugs and the eukaryotic ribosome, we propose a unifying hypothesis for read-through enhancement by small molecules, highlighting the role of decoding center rearrangements and intersubunit rotation dynamics. | ||||||||||||
| 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_50990.map.gz | 1.2 GB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-50990-v30.xml emd-50990.xml | 101.5 KB 101.5 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_50990_fsc.xml | 23 KB | 表示 | FSCデータファイル |
| 画像 | emd_50990.png | 121.8 KB | ||
| Filedesc metadata | emd-50990.cif.gz | 19.5 KB | ||
| その他 | emd_50990_half_map_1.map.gz emd_50990_half_map_2.map.gz | 1.2 GB 1.2 GB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-50990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50990 | HTTPS FTP |
-検証レポート
| 文書・要旨 | emd_50990_validation.pdf.gz | 1.3 MB | 表示 | EMDB検証レポート |
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| 文書・詳細版 | emd_50990_full_validation.pdf.gz | 1.3 MB | 表示 | |
| XML形式データ | emd_50990_validation.xml.gz | 32.7 KB | 表示 | |
| CIF形式データ | emd_50990_validation.cif.gz | 43.4 KB | 表示 | |
| アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50990 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50990 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9g30MC ![]() 9g1zC ![]() 9g6jC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_50990.map.gz / 形式: CCP4 / 大きさ: 1.3 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | Cryo-EM map of the Candida albicans ribosome in complex with mRNA and initiator tRNA (strong A site tRNA), and two compounds. | ||||||||||||||||||||||||||||||||||||
| 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: 0.729 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: Half map A
| ファイル | emd_50990_half_map_1.map | ||||||||||||
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| 注釈 | Half map A | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: Half map B
| ファイル | emd_50990_half_map_2.map | ||||||||||||
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| 注釈 | Half map B | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
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試料の構成要素
+全体 : Candida albicans ribosome in complex with initiator fMet-tRNA, mR...
+超分子 #1: Candida albicans ribosome in complex with initiator fMet-tRNA, mR...
+分子 #1: 60S ribosomal protein L20
+分子 #3: 60S ribosomal protein L21-A
+分子 #6: 60S ribosomal protein L23-A
+分子 #7: 60S ribosomal protein L24-A
+分子 #8: 60S ribosomal protein L25
+分子 #9: Ribosomal protein L24
+分子 #11: 40S ribosomal protein S0
+分子 #12: 40S ribosomal protein S1
+分子 #13: Ribosomal protein S5
+分子 #14: Ribosomal protein S3
+分子 #15: 40S ribosomal protein S4
+分子 #16: Ribosomal protein S7
+分子 #17: 40S ribosomal protein S6
+分子 #18: 40S ribosomal protein S7
+分子 #19: 40S ribosomal protein S8
+分子 #20: Ribosomal protein S4
+分子 #21: 40S ribosomal protein S10-A
+分子 #22: 40S ribosomal protein S11A
+分子 #23: 40S ribosomal protein S12
+分子 #24: 40S ribosomal protein S13
+分子 #25: 40S ribosomal protein S14-A
+分子 #26: 40S ribosomal protein S15
+分子 #27: 40S ribosomal protein S18-B
+分子 #28: 40S ribosomal protein S16
+分子 #29: 40S ribosomal protein S17-B
+分子 #30: 40S ribosomal protein S19-A
+分子 #31: Ribosomal protein S10
+分子 #32: 40S ribosomal protein S21
+分子 #33: 40S ribosomal protein S22-A
+分子 #34: Ribosomal protein S23 (S12)
+分子 #35: 40S ribosomal protein S24
+分子 #36: 40S ribosomal protein S25
+分子 #37: 40S ribosomal protein S26
+分子 #38: 40S ribosomal protein S27
+分子 #39: 40S ribosomal protein S28-B
+分子 #40: 40S ribosomal protein S29A
+分子 #41: 40S ribosomal protein S30
+分子 #42: Ubiquitin-40S ribosomal protein S31 fusion protein
+分子 #43: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #44: 60S ribosomal protein L2-B
+分子 #45: 60S ribosomal protein L3
+分子 #46: 60S ribosomal protein L4-B
+分子 #47: 60S ribosomal protein L5
+分子 #48: 60S ribosomal protein L6
+分子 #49: 60S ribosomal protein L7-A
+分子 #50: 60S ribosomal protein L8
+分子 #51: 60S ribosomal protein L9-B
+分子 #52: 60S ribosomal protein L10
+分子 #53: 60S ribosomal protein L11-B
+分子 #54: 60S ribosomal protein L13
+分子 #55: 60S ribosomal protein L14-B
+分子 #56: 60S ribosomal protein L15-A
+分子 #57: Ribosomal protein L13
+分子 #58: Ribosomal protein L22
+分子 #59: 60S ribosomal protein L18-A
+分子 #60: 60S ribosomal protein L19-A
+分子 #61: 60S ribosomal protein L27
+分子 #62: 60S ribosomal protein L28
+分子 #63: 60S ribosomal protein L29
+分子 #64: 60S ribosomal protein L30
+分子 #65: 60S ribosomal protein L31-B
+分子 #66: 60S ribosomal protein L32
+分子 #67: 60S ribosomal protein L33-A
+分子 #68: 60S ribosomal protein L34-B
+分子 #69: Ribosomal protein L29
+分子 #70: 60S ribosomal protein L36
+分子 #71: 60S ribosomal protein L37-B
+分子 #72: 60S ribosomal protein L38
+分子 #73: 60S ribosomal protein L39
+分子 #74: 60S ribosomal protein L40-B
+分子 #75: 60S ribosomal protein L41
+分子 #76: 60S ribosomal protein L42-B
+分子 #77: 60S ribosomal protein L43-A
+分子 #2: 25S rRNA
+分子 #4: 5S rRNA
+分子 #5: 5.8S rRNA
+分子 #10: 18S rRNA
+分子 #78: tRNA
+分子 #79: mRNA
+分子 #80: SPERMINE (FULLY PROTONATED FORM)
+分子 #81: GENETICIN
+分子 #82: 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 |
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試料調製
| 緩衝液 | pH: 7.5 |
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| 凍結 | 凍結剤: ETHANE |
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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 IV (4k x 4k) 平均電子線量: 29.7 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.2 µm / 最小 デフォーカス(公称値): 0.2 µm |
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
ムービー
コントローラー
万見について




キーワード
Candida albicans SC5314 (酵母)
データ登録者
フランス, 3件
引用
















Z (Sec.)
Y (Row.)
X (Col.)






































解析
FIELD EMISSION GUN


