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- PDB-9lb0: Cryo-EM structure of the MK7-bound succinate dehydrogenase from C... -

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Basic information

Entry
Database: PDB / ID: 9lb0
TitleCryo-EM structure of the MK7-bound succinate dehydrogenase from Chloroflexus aurantiacus
Components
  • (Succinate dehydrogenase ...) x 2
  • 4Fe-4S ferredoxin iron-sulfur binding domain protein
KeywordsMEMBRANE PROTEIN / Succinate: menaquinone oxidoreductase / 3-hydroxypropionate cycle / succinate dehydrogenase / electron transfer
Function / homology
Function and homology information


steroid dehydrogenase activity, acting on the CH-CH group of donors / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity ...steroid dehydrogenase activity, acting on the CH-CH group of donors / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
Succinate dehydrogenase cytochrome b558 subunit / Succinate dehydrogenase/fumarate reductase flavoprotein subunit, low-GC Gram-positive bacteria / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 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 cytochrome b558 subunit / Succinate dehydrogenase/fumarate reductase flavoprotein subunit, low-GC Gram-positive bacteria / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 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 / 4Fe-4S dicluster domain / 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 / MENAQUINONE-7 / IRON/SULFUR CLUSTER / 4Fe-4S ferredoxin iron-sulfur binding domain protein / succinate dehydrogenase / Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsZhang, X. / Wu, J.Y. / Xu, X.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471270 China
National Natural Science Foundation of China (NSFC)32171227 China
National Natural Science Foundation of China (NSFC)31870740 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of menaquinone reduction by succinate dehydrogenase from Chloroflexus aurantiacus.
Authors: Xin Zhang / Jingyi Wu / Jiamao Wang / Huimin He / Aokun Liu / Xin Hong / Yuanyi Yu / Xinkai Pei / Xianjie Fang / Yueyong Xin / Lu Yu / Changlin Tian / Xiaoling Xu /
Abstract: Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing ...Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing bacteria and archaea. Despite its significance, questions persist regarding the electron and proton transfer mechanisms that drive the endergonic MK reduction by succinate. In this study, we determine cryo-EM structures of succinate dehydrogenase (SDH) from Chloroflexus aurantiacus (CaSDH), a facultative filamentous anoxygenic phototroph (FAP) that forms one of the earliest branches of photosynthetic bacteria. The structures of trimeric CaSDH, resolved in both apo- and MK-bound forms, reveal a single membrane-anchoring subunit containing two b-type hemes, a canonical Q site, and a Q site with atypical location, configuration and specificity, each bound to MK molecules. Using structural analysis, EPR, and enzymatic assays, we uncover electron transfer pathways connecting succinate oxidation to MK reduction at the Q and Q sites. These findings provide structural insights into the electron and proton transfer mechanisms of MK-dependent diheme SQRs and establish a foundation for structure-based inhibitor design and antibacterial drug development targeting these enzymes.
History
DepositionJan 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 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 or fumarate reductase, flavoprotein subunit
B: 4Fe-4S ferredoxin iron-sulfur binding domain protein
C: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
D: Succinate dehydrogenase or fumarate reductase, flavoprotein subunit
E: 4Fe-4S ferredoxin iron-sulfur binding domain protein
F: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
G: Succinate dehydrogenase or fumarate reductase, flavoprotein subunit
H: 4Fe-4S ferredoxin iron-sulfur binding domain protein
I: Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,82936
Polymers385,8789
Non-polymers13,95127
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 ... , 2 types, 6 molecules ADGCFI

#1: Protein Succinate dehydrogenase or fumarate reductase, flavoprotein subunit


Mass: 73373.930 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WDT7, EC: 1.3.99.1
#3: Protein Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family


Mass: 27141.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WDT8

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Protein / Sugars , 2 types, 6 molecules BEH

#2: Protein 4Fe-4S ferredoxin iron-sulfur binding domain protein


Mass: 28110.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WDT6
#9: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 6 types, 24 molecules

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


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H64O2 / Feature type: SUBJECT OF INVESTIGATION

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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 apo-form succinate dehydrogenase from Chloroflexus aurantiacus
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Buffer solutionpH: 8
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 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 / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25554 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00527848
ELECTRON MICROSCOPYf_angle_d0.5637868
ELECTRON MICROSCOPYf_dihedral_angle_d7.5733908
ELECTRON MICROSCOPYf_chiral_restr0.0434029
ELECTRON MICROSCOPYf_plane_restr0.0044860

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