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- PDB-9fqk: Perkinsus marinus Respiratory complex II soluble region -

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Basic information

Entry
Database: PDB / ID: 9fqk
TitlePerkinsus marinus Respiratory complex II soluble region
Components(Succinate dehydrogenase [ubiquinone] ...) x 2
KeywordsMEMBRANE PROTEIN / Respiratory complex / complex II soluble region
Function / homologyFE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / : / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesPerkinsus marinus (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWu, F. / Amunts, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
CitationJournal: To Be Published
Title: Perkinsus marinus Respiratory complex II soluble region
Authors: Wu, F. / Amunts, A.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2m: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
2n: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9157
Polymers95,2682
Non-polymers1,6485
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] ... , 2 types, 2 molecules 2m2n

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial


Mass: 65587.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial


Mass: 29680.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: succinate dehydrogenase

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Non-polymers , 5 types, 5 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe3S4
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION

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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: Respiratory complex / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Perkinsus marinus (eukaryote)
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296890 / Symmetry type: POINT

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