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- PDB-8k6k: Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from G... -

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Basic information

Entry
Database: PDB / ID: 8k6k
TitleCryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146A
Components(Fructose dehydrogenase ...) x 3
KeywordsOXIDOREDUCTASE / Complex / OXIDOREDUCTASE Membrane-bound protein / OXIDEREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / fructose metabolic process / 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 / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / HEME C / UBIQUINONE-10 / Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase small subunit
Similarity search - Component
Biological speciesGluconobacter japonicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsFukawa, E. / Miyata, T. / Makino, F. / Adachi, T. / Suzuki, Y. / 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: Electrochim Acta / Year: 2024
Title: Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase.
Authors: Fukawa, E. / Suzuki, Y. / Adachi, T. / Miyata, T. / Makino, F. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose dehydrogenase (N1146A) large subunit
B: Fructose dehydrogenase small subunit
C: Fructose dehydrogenase cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9159
Polymers132,1153
Non-polymers3,8006
Water00
1


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

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Components

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

#1: Protein Fructose dehydrogenase (N1146A) large subunit


Mass: 59755.285 Da / Num. of mol.: 1 / Mutation: N1146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhL / Production host: Gluconobacter oxydans (bacteria) / References: 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


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


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


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
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: D-fructose dehydrogenase (N1146A) 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-MercaptethanolC2H6OS1
SpecimenConc.: 3.6 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 FIELD / 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: 50 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: 9439
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.0particle selection
2SerialEM3.9image acquisition
4cryoSPARC4.2.0CTF correction
8PHENIXmodel refinement
10cryoSPARC4.2.0initial Euler assignment
11cryoSPARC4.2.0final Euler assignment
12cryoSPARC4.2.0classification
13cryoSPARC4.2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2982801
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355363 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038835
ELECTRON MICROSCOPYf_angle_d1.03512078
ELECTRON MICROSCOPYf_dihedral_angle_d10.7321277
ELECTRON MICROSCOPYf_chiral_restr0.0611277
ELECTRON MICROSCOPYf_plane_restr0.0041562

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