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データを開く
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基本情報
| 登録情報 | データベース: PDB / ID: 9kps | |||||||||||||||||||||
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| タイトル | Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II | |||||||||||||||||||||
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キーワード | MEMBRANE PROTEIN / Complex / mitochondria / ELECTRON TRANSPORT | |||||||||||||||||||||
| 機能・相同性 | 機能・相同性情報Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cellular respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / quinone binding ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cellular respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / quinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding 類似検索 - 分子機能 | |||||||||||||||||||||
| 生物種 | ![]() | |||||||||||||||||||||
| 手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.36 Å | |||||||||||||||||||||
データ登録者 | Li, Z.W. / Ye, Y. / Yang, G.F. | |||||||||||||||||||||
| 資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2025タイトル: Cryo-EM structure of the yeast Saccharomyces cerevisiae SDH provides a template for eco-friendly fungicide discovery. 著者: Zhi-Wen Li / Yuan-Hui Huang / Ge Wei / Zong-Wei Lu / Yu-Xia Wang / Guang-Rui Cui / Jun-Ya Wang / Xin-He Yu / Yi-Xuan Fu / Er-Di Fan / Qiong-You Wu / Xiao-Lei Zhu / Ying Ye / Guang-Fu Yang / ![]() 要旨: Succinate dehydrogenase (SDH) is a key fungicidal target, but rational inhibitors design has been impeded by the lack of fungal SDH structure. Here, we show the cryo-EM structure of SDH from ...Succinate dehydrogenase (SDH) is a key fungicidal target, but rational inhibitors design has been impeded by the lack of fungal SDH structure. Here, we show the cryo-EM structure of SDH from Saccharomyces cerevisiae (ScSDH) in apo (3.36 Å) and ubiquinone-1-bound (3.25 Å) states, revealing subunits architecture and quinone-binding sites (Q). ScSDH is classified as a heme-deficient type-D SDH, utilizing conserved redox centers (FAD, [2Fe-2S], [4Fe-4S] and [3Fe-4S] clusters) for electron transfer. A 3.23 Å structure with pydiflumetofen (PYD) identified critical interactions, including hydrogen bonds with Trp_SDHB194 and Tyr_SDHD120, and a cation-π interaction with Arg_SDHC97. Leveraging this, we designed a SDH inhibitor E8 (enprocymid), exhibiting significant fungicidal activity (K = 0.019 μM) and reduced zebrafish toxicity (LC (96 h) = 1.01 mg a.i./L). This study elucidates the structure of fungal SDH and demonstrates the potential of ScSDH for rational design of next-generation fungicides, addressing fungal resistance and environmental toxicity in agriculture. | |||||||||||||||||||||
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構造の表示
| 構造ビューア | 分子: Molmil Jmol/JSmol |
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ダウンロードとリンク
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ダウンロード
| PDBx/mmCIF形式 | 9kps.cif.gz | 212.4 KB | 表示 | PDBx/mmCIF形式 |
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| PDB形式 | pdb9kps.ent.gz | 163.4 KB | 表示 | PDB形式 |
| PDBx/mmJSON形式 | 9kps.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
| その他 | その他のダウンロード |
-検証レポート
| 文書・要旨 | 9kps_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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| 文書・詳細版 | 9kps_full_validation.pdf.gz | 1.3 MB | 表示 | |
| XML形式データ | 9kps_validation.xml.gz | 44.5 KB | 表示 | |
| CIF形式データ | 9kps_validation.cif.gz | 65.8 KB | 表示 | |
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kp/9kps ftp://data.pdbj.org/pub/pdb/validation_reports/kp/9kps | HTTPS FTP |
-関連構造データ
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リンク
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集合体
| 登録構造単位 | ![]()
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| 1 |
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要素
-Succinate dehydrogenase [ubiquinone] ... , 3種, 3分子 ABD
| #1: タンパク質 | 分子量: 65307.602 Da / 分子数: 1 / 由来タイプ: 天然 詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces ...詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces cerevisiae strain RedStar is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q00711. 由来: (天然) ![]() |
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| #2: タンパク質 | 分子量: 27332.654 Da / 分子数: 1 / 由来タイプ: 天然 詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces ...詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces cerevisiae strain RedStar is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID P21801. 由来: (天然) ![]() |
| #4: タンパク質 | 分子量: 14799.092 Da / 分子数: 1 / 由来タイプ: 天然 詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces ...詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces cerevisiae strain RedStar is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID P37298. 由来: (天然) ![]() |
-タンパク質 , 1種, 1分子 C
| #3: タンパク質 | 分子量: 16396.133 Da / 分子数: 1 / 由来タイプ: 天然 詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces ...詳細: The sample used was sourced from Saccharomyces cerevisiae (Tax ID: 4932), strain Redstar, with the GenBank ID in the SGD database being JRIL00000000. Sequence reference for Saccharomyces cerevisiae strain RedStar is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID C7GVH5. 由来: (天然) ![]() |
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-非ポリマー , 5種, 5分子 








| #5: 化合物 | ChemComp-FAD / |
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| #6: 化合物 | ChemComp-FES / |
| #7: 化合物 | ChemComp-SF4 / |
| #8: 化合物 | ChemComp-F3S / |
| #9: 化合物 | ChemComp-PEE / |
-詳細
| 研究の焦点であるリガンドがあるか | N |
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| Has protein modification | N |
-実験情報
-実験
| 実験 | 手法: 電子顕微鏡法 |
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| EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
| 構成要素 | 名称: Mitochondrial Respiratory Complex II / タイプ: COMPLEX / Entity ID: #1-#4 / 由来: NATURAL |
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| 由来(天然) | 生物種: ![]() |
| 緩衝液 | pH: 7.4 |
| 試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
| 急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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| 顕微鏡 | モデル: TFS KRIOS |
| 電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
| 電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1200 nm |
| 撮影 | 電子線照射量: 48.94 e/Å2 フィルム・検出器のモデル: TFS FALCON 4i (4k x 4k) |
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解析
| CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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| 3次元再構成 | 解像度: 3.36 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 79821 / 対称性のタイプ: POINT |
| 原子モデル構築 | プロトコル: AB INITIO MODEL |
| 精密化 | 最高解像度: 3.36 Å |
ムービー
コントローラー
万見について






中国, 1件
引用






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FIELD EMISSION GUN