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- PDB-7w2j: Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from G... -

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Basic information

Entry
Database: PDB / ID: 7w2j
TitleCryo-EM Structure of 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 ...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 oxidase, cbb3-type, subunit III / 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 / 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: 3.6 Å
AuthorsSuzuki, Y. / Makino, F. / Miyata, T. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01961 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
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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
D: Fructose dehydrogenase large subunit
E: Fructose dehydrogenase small subunit
F: Fructose dehydrogenase cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,18916
Polymers264,3156
Non-polymers5,87410
Water00
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, 6 molecules ADBECF

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


Mass: 59798.309 Da / Num. of mol.: 2
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.: 2
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.: 2
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 , 3 types, 10 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#6: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / 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
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 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: 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: 2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5575
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1Warp1.09particle selection
2SerialEM3.9image acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 365385
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91745 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00916972
ELECTRON MICROSCOPYf_angle_d0.97223202
ELECTRON MICROSCOPYf_dihedral_angle_d8.9732346
ELECTRON MICROSCOPYf_chiral_restr0.0532476
ELECTRON MICROSCOPYf_plane_restr0.0062986

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