9KPT
Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in UQ1-bound state
Summary for 9KPT
| Entry DOI | 10.2210/pdb9kpt/pdb |
| EMDB information | 62491 |
| Descriptor | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial, ... (10 entities in total) |
| Functional Keywords | complex, mitochondria, electron transport, membrane protein |
| Biological source | Saccharomyces cerevisiae (brewer's yeast) More |
| Total number of polymer chains | 4 |
| Total formula weight | 125912.99 |
| Authors | Li, Z.W.,Ye, Y.,Yang, G.F. (deposition date: 2024-11-24, release date: 2025-09-03, Last modification date: 2025-10-22) |
| Primary citation | Li, Z.W.,Huang, Y.H.,Wei, G.,Lu, Z.W.,Wang, Y.X.,Cui, G.R.,Wang, J.Y.,Yu, X.H.,Fu, Y.X.,Fan, E.D.,Wu, Q.Y.,Zhu, X.L.,Ye, Y.,Yang, G.F. Cryo-EM structure of the yeast Saccharomyces cerevisiae SDH provides a template for eco-friendly fungicide discovery. Nat Commun, 16:8936-8936, 2025 Cited by PubMed Abstract: 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. PubMed: 41062466DOI: 10.1038/s41467-025-64001-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.25 Å) |
Structure validation
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