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- PDB-8jek: Cryo-EM Structure of K-ferricyanide Oxidized Membrane-bound Fruct... -

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Basic information

Entry
Database: PDB / ID: 8jek
TitleCryo-EM Structure of K-ferricyanide Oxidized Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus
Components(Fructose dehydrogenase ...) x 3
KeywordsOXIDOREDUCTASE / Complex / OXIDOREDUCTASE Membrane-bound protein
Function / homology
Function and homology information


fructose 5-dehydrogenase / fructose 5-dehydrogenase activity / oxidoreductase activity, acting on CH-OH group of donors / fructose metabolic process / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Cytochrome c / Cytochrome c family profile. ...FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / HEME C / UBIQUINONE-10 / Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase small subunit / Fructose dehydrogenase large subunit
Similarity search - Component
Biological speciesGluconobacter japonicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSuzuki, Y. / Miyata, T. / Makino, F. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01961 Japan
Japan Society for the Promotion of Science (JSPS)JP22K14831 Japan
CitationJournal: Acs Catalysis / Year: 2023
Title: Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry.
Authors: Suzuki, Y. / Makino, F. / Miyata, T. / Tanaka, H. / Namba, K. / Kano, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
History
DepositionMay 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose dehydrogenase large subunit
B: Fructose dehydrogenase small subunit
C: Fructose dehydrogenase cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9589
Polymers132,1583
Non-polymers3,8006
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Fructose dehydrogenase ... , 3 types, 3 molecules ABC

#1: Protein Fructose dehydrogenase large subunit / Fructose dehydrogenase subunit I


Mass: 59798.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhL / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1VMF7, EC: 1.1.99.11
#2: Protein Fructose dehydrogenase small subunit / Fructose dehydrogenase subunit III


Mass: 20106.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhS / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1VB40
#3: Protein Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase subunit II


Mass: 52252.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhC / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1V1V5

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Non-polymers , 4 types, 6 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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
#5: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#6: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: D-fructose dehydrogenase from Gluconobacter japonicus / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: YES
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Source (recombinant)Organism: Gluconobacter oxydans (bacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
1176 mmol / LSodium dihydrogen phosphateNaH2PO41
224 mmol / LSodium hydrogen phosphateNa2HPO41
31.5 mmol / L2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanolC14H22O(C2H4O)n1
41 mmol / L2-MercaptoethanolC2H6OS1
51 mmol / LPotassium ferricyanideC6FeK3N61
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Calibrated magnification: 56754 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 40 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 0.01 mradians
Image recordingAverage exposure time: 3 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4650
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
2SerialEM3.9image acquisition
4cryoSPARC3.3.2CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 731576
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 448071 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048857
ELECTRON MICROSCOPYf_angle_d0.66612104
ELECTRON MICROSCOPYf_dihedral_angle_d11.1951339
ELECTRON MICROSCOPYf_chiral_restr0.0461278
ELECTRON MICROSCOPYf_plane_restr0.0071574

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