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Entry
Database: EMDB / ID: EMD-62495
TitleCryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state
Map data
Sample
  • Complex: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
    • Protein or peptide: Sdh3p
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: Pydiflumetofen
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
KeywordsComplex / mitochondria / ELECTRON TRANSPORT / MEMBRANE PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsLi ZW / Ye Y / Yang GF
Funding support China, 1 items
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 25, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62495.png

Downloads & links

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Map

FileDownload / File: emd_62495.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 384 pix.
= 288. Å		0.75 Å/pix.
x 384 pix.
= 288. Å		0.75 Å/pix.
x 384 pix.
= 288. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.364
Minimum - Maximum-1.1954713 - 2.4136195
Average (Standard dev.)0.00084163813 (±0.038679767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62495_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62495_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respi...

EntireName: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state
Components
  • Complex: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
    • Protein or peptide: Sdh3p
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: Pydiflumetofen
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respi...

SupramoleculeName: Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RedStar

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Macromolecule #1: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
type: protein_or_peptide / ID: 1
Details: Sequence reference for Saccharomyces cerevisiae (strain RedStar) is not available at the time of biocuration. Current sequence reference is from UniProt id Q00711.
Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RedStar
Molecular weightTheoretical: 65.699047 KDa
SequenceString: KYHIIDHEYD CVVIGAGGAG LRAAFGLAEA GYKTACISKL FPTRSHTVAA QGGINAALGN MHKDNWKWHM YDTVKGSDWL GDQDSIHYM TREAPKSIIE LEHYGVPFSR TENGKIYQRA FGGQTKEYGK GAQAYRTCAV ADRTGHALLH TLYGQALRHD T HFFIEYFA ...String:
KYHIIDHEYD CVVIGAGGAG LRAAFGLAEA GYKTACISKL FPTRSHTVAA QGGINAALGN MHKDNWKWHM YDTVKGSDWL GDQDSIHYM TREAPKSIIE LEHYGVPFSR TENGKIYQRA FGGQTKEYGK GAQAYRTCAV ADRTGHALLH TLYGQALRHD T HFFIEYFA LDLLTHNGEV VGVIAYNQED GTIHRFRAHK TIIATGGYGR AYFSCTSAHT CTGDGNAMVS RAGFPLQDLE FV QFHPSGI YGSGCLITEG ARGEGGFLVN SEGERFMERY APTAKDLACR DVVSRAITME IREGRGVGKK KDHMYLQLSH LPP EVLKER LPGISETAAI FAGVDVTKEP IPIIPTVHYN MGGIPTKWNG EALTIDEETG EDKVIPGLMA CGEAACVSVH GANR LGANS LLDLVVFGRA VAHTVADTLQ PGLPHKPLPS DLGKESIANL DKLRNANGSR STAEIRMNMK QTMQKDVSVF RTQSS LDEG VRNITAVEKT FDDVKTTDRS MIWNSDLVET LELQNLLTCA SQTAVSAANR KESRGAHARE DYPNRDDEHW MKHTLS WQK DVAAPVTLKY RRVIDHTLDE KECPSVPPTV RAY

UniProtKB: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

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Macromolecule #2: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitocho...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
type: protein_or_peptide / ID: 2
Details: Sequence reference for Saccharomyces cerevisiae (strain RedStar) is not available at the time of biocuration. Current sequence reference is from UniProt id P21801.
Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RedStar
Molecular weightTheoretical: 27.0934 KDa
SequenceString: TPRLKTFKVY RWNPDEPSAK PHLQSYQVDL NDCGPMVLDA LLKIKDEQDS TLTFRRSCRE GICGSCAMNI GGRNTLACIC KIDQNESKQ LKIYPLPHMF IVKDLVPDLT NFYQQYKSIQ PYLQRSSFPK DGTEVLQSIE DRKKLDGLYE CILCACCSTS C PSYWWNQE ...String:
TPRLKTFKVY RWNPDEPSAK PHLQSYQVDL NDCGPMVLDA LLKIKDEQDS TLTFRRSCRE GICGSCAMNI GGRNTLACIC KIDQNESKQ LKIYPLPHMF IVKDLVPDLT NFYQQYKSIQ PYLQRSSFPK DGTEVLQSIE DRKKLDGLYE CILCACCSTS C PSYWWNQE QYLGPAVLMQ AYRWLIDSRD QATKTRKAML NNSMSLYRCH TIMNCTRTCP KGLNPGLAIA EIKKSLAF

UniProtKB: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

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Macromolecule #3: Sdh3p

MacromoleculeName: Sdh3p / type: protein_or_peptide / ID: 3
Details: Sequence reference for Saccharomyces cerevisiae (strain RedStar) is not available at the time of biocuration. Current sequence reference is from UniProt id C7GVH5.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RedStar
Molecular weightTheoretical: 16.26702 KDa
SequenceString:
MNTKAAIAEE QILNKQRARR PISPHLTIYQ PQLTWYLSSF HRISLVLMGL GFYLFTILFG VSGLLGLGLT TEKVSNWYHQ KFSKITEWS IKGSFAYLFA IHYGGAIRHL IWDTAKELTL KGVYRTGYAL IGFTAVLGTY LLTL

UniProtKB: Sdh3p

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Macromolecule #4: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, ...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
type: protein_or_peptide / ID: 4
Details: Sequence reference for Saccharomyces cerevisiae (strain RedStar) is not available at the time of biocuration. Current sequence reference is from UniProt id P37298.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RedStar
Molecular weightTheoretical: 14.441644 KDa
SequenceString:
LPVLPQKPGG VRGTPNDAYV PPPENKLEGS YHWYMEKIFA LSVVPLATTA MLTTGPLSTA ADSFFSVMLL GYCYMEFNSC ITDYISGRV YGVWHKYAMY MLGLGSAVSL FGIYKLETEN DGVVGLVKSL WD

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #9: Pydiflumetofen

MacromoleculeName: Pydiflumetofen / type: ligand / ID: 9 / Number of copies: 1 / Formula: A1EE4
Molecular weightTheoretical: 426.673 Da

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Macromolecule #10: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 10 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.11 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9kq3:
Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state

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