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- PDB-9qdl: CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II -

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Entry
Database: PDB / ID: 9qdl
TitleCRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II
Components(Succinate dehydrogenase [ubiquinone] ...) x 4
KeywordsOXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / UBIQUINONE-1
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / quinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / 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 / Succinate dehydrogenase/fumarate reductase, flavoprotein 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 / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / hexacosanoic acid / : / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / : / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial ...1,2-Distearoyl-sn-glycerophosphoethanolamine / hexacosanoic acid / : / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / : / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b 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)
Saccharomyces cerevisiae W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsPinotsis, N. / Marechal, A. / Berry, E.A. / Shu, C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T032154/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structure of bixafen-bound S. cerevisiae complex II unravels SDHI specificity against pathogenic fungi.
Authors: Nikos Pinotsis / Claudia Burn-Leefe / Sarah Jones / Shu Chen / Natalya Lukoyanova / Brigitte Meunier / Edward A Berry / Amandine Maréchal /
Abstract: Respiratory complex II (CII), or succinate dehydrogenase, couples succinate oxidation in the Krebs cycle with electron transfer to the respiratory chain. Owing to this pivotal role, CII inhibitors ...Respiratory complex II (CII), or succinate dehydrogenase, couples succinate oxidation in the Krebs cycle with electron transfer to the respiratory chain. Owing to this pivotal role, CII inhibitors are widely used fungicides globally; however, their development has largely proceeded without structural insights from fungal targets. Here, we report cryo-electron microscopy structures of the 128 kDa mitochondrial CII from Saccharomyces cerevisiae in two states: active, with endogenous ubiquinone-6 bound (3.15 Å), and inhibited with the fungicide bixafen (3.00 Å). Although closely related to the mammalian type C enzyme, our structures show that the yeast CII has lost the canonical heme cofactor. They also reveal how clade-specific sequence extensions of the membrane subunits Sdh3 and Sdh4 - conserved in pathogenic fungi - uniquely contribute to complex stability and fungicide binding. Our findings provide a foundation for rational design of next-generation CII inhibitors and combatting resistance, in both agriculture and human health.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,38412
Polymers145,0004
Non-polymers3,3848
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Succinate dehydrogenase [ubiquinone] ... , 4 types, 4 molecules ABCD

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


Mass: 70404.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SDH1, SDHA, YKL148C, YKL602 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ATCC 204508 / S288c / References: UniProt: Q00711, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 30347.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SDH2, SDH, SDHB, YLL041C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ATCC 204508 / S288c / References: UniProt: P21801, succinate dehydrogenase
#3: Protein Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial


Mass: 22167.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The specific variant has the following modifications compared to P33421: Ser14Pro Lys74Arg Leu95Phe
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508/S288c / Gene: SDH3, CYB3, YKL141W, YKL4 / Production host: Saccharomyces cerevisiae W303 (yeast) / Strain (production host): ATCC 204508/S288c / References: UniProt: P33421
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 22081.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Modified with an N-terminal His-Tag
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508/S288c / Gene: SDH4, ACN18, YDR178W, YD9395.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ATCC 204508/S288c / References: UniProt: P37298

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Non-polymers , 9 types, 26 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-A1J2J / Ubiquinone-6 / 2-[(2E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaenyl]-5,6-dimethoxy-3-methyl-cyclohexa-2,5-diene-1,4-dione


Mass: 590.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H58O4
#11: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-7PO / hexacosanoic acid


Mass: 396.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C26H52O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.128 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.2 / Details: 150 mM NaCl 0.05% GDN
Buffer componentConc.: 50 mM / Name: HEPES
SpecimenConc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 279 K

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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 magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 18.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 20000
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149808 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11AF-Q007111AlphaFoldin silico model
21AF-P218012AlphaFoldin silico model
31AF-P334213AlphaFoldin silico model
41AF-P372984AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00358309
ELECTRON MICROSCOPYf_angle_d0.527511273
ELECTRON MICROSCOPYf_chiral_restr0.04071232
ELECTRON MICROSCOPYf_plane_restr0.00471420
ELECTRON MICROSCOPYf_dihedral_angle_d10.88111247

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