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- PDB-9kc4: The Cryo-EM structure of human succinate dehydrogenase in complex... -

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Basic information

Entry
Database: PDB / ID: 9kc4
TitleThe Cryo-EM structure of human succinate dehydrogenase in complex with Benzovindiflupyr
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


regulation of catecholamine secretion / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport ...regulation of catecholamine secretion / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / mitochondrial envelope / 3 iron, 4 sulfur cluster binding / ubiquinone binding / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / flavin adenine dinucleotide binding / nervous system development / 4 iron, 4 sulfur cluster binding / cellular response to hypoxia / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / heme binding / nucleolus / mitochondrion / nucleoplasm / membrane / metal ion binding / plasma membrane
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
: / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-PEV / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsLiu, Y. / Gong, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: To Be Published
Title: The Cryo-EM structure of human succinate dehydrogenase in complex with Benzovindiflupyr
Authors: Liu, Y. / Gong, H.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 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

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: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,50111
Polymers140,1574
Non-polymers3,3447
Water00
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] ... , 3 types, 3 molecules ABD

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


Mass: 72786.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHA, SDH2, SDHF / Production host: Homo sapiens (human)
References: UniProt: P31040, succinate dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip / Malate dehydrogenase [quinone] iron-sulfur subunit


Mass: 31674.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHB, SDH, SDH1 / Production host: Homo sapiens (human)
References: UniProt: P21912, succinate dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / CII-4 / Malate dehydrogenase [quinone] cytochrome b small subunit / QPs3 / Succinate ...CybS / CII-4 / Malate dehydrogenase [quinone] cytochrome b small subunit / QPs3 / Succinate dehydrogenase complex subunit D / Succinate-ubiquinone oxidoreductase cytochrome b small subunit / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 17063.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHD, SDH4 / Production host: Homo sapiens (human) / References: UniProt: O14521

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Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Integral membrane protein CII-3 / Malate dehydrogenase [quinone] cytochrome b560 subunit / QPs-1 / ...Integral membrane protein CII-3 / Malate dehydrogenase [quinone] cytochrome b560 subunit / QPs-1 / QPs1 / Succinate dehydrogenase complex subunit C / Succinate-ubiquinone oxidoreductase cytochrome B large subunit / CYBL


Mass: 18632.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHC, CYB560, SDH3 / Production host: Homo sapiens (human) / References: UniProt: Q99643

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Non-polymers , 7 types, 7 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-A1EGM / (1S,4R)-benzovindiflupyr / SCHEMBL679304


Mass: 398.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15Cl2F2N3O / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM

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Details

Has ligand of interestY
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: the human respiratory complex II with Benzovindiflupyr
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129695 / Symmetry type: POINT
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038850
ELECTRON MICROSCOPYf_angle_d0.55312013
ELECTRON MICROSCOPYf_dihedral_angle_d8.6111280
ELECTRON MICROSCOPYf_chiral_restr0.041298
ELECTRON MICROSCOPYf_plane_restr0.0031519

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