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- PDB-9kps: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respi... -

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Basic information

Entry
Database: PDB / ID: 9kps
TitleCryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Sdh3p
KeywordsMEMBRANE PROTEIN / Complex / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


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
Similarity search - Function
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / IRON/SULFUR CLUSTER / Sdh3p / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsLi, Z.W. / Ye, Y. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure of the yeast Saccharomyces cerevisiae SDH provides a template for eco-friendly fungicide discovery.
Authors: 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 /
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 ...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.
History
DepositionNov 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Sdh3p
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1889
Polymers123,8354
Non-polymers2,3535
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Flavoprotein subunit of complex II / FP


Mass: 65307.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 ...Details: 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.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: Redstar / References: UniProt: Q00711, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 27332.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 ...Details: 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.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: Redstar / References: UniProt: P21801, succinate dehydrogenase
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 14799.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 ...Details: 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.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: Redstar / References: UniProt: P37298

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Protein , 1 types, 1 molecules C

#3: Protein Sdh3p / Succinate dehydrogenase [ubiquinone] cytochrome b subunit / mitochondrial


Mass: 16396.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 ...Details: 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.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: Redstar / References: UniProt: C7GVH5

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Non-polymers , 5 types, 5 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial Respiratory Complex II / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: Redstar
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48.94 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79821 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.36 Å

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