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- EMDB-61725: Cryo-EM Structure of Fructose Dehydrogenase Variant from Gluconob... -

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Basic information

Entry
Database: EMDB / ID: EMD-61725
TitleCryo-EM Structure of Fructose Dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-Terminal Hydrophobic Regions
Map data
Sample
  • Complex: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions
    • Protein or peptide: Fructose dehydrogenase large subunit
    • Protein or peptide: Fructose dehydrogenase small subunit
    • Protein or peptide: Fructose dehydrogenase cytochrome subunit
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: HEME C
KeywordsComplex / OXIDOREDUCTASE Membrane-bound protein / OXIDOREDUCTASE
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
Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase small subunit / Fructose dehydrogenase large subunit
Similarity search - Component
Biological speciesGluconobacter japonicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsAdachi T / Ichikawa K / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Shirai O
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
Japan Society for the Promotion of Science (JSPS)JP23K19281 Japan
Japan Society for the Promotion of Science (JSPS)JP22K14831 Japan
CitationJournal: ACS Electrochem / Year: 2025
Title: Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1c and C-Terminal Hydrophobic Regions
Authors: Adachi T / Ichikawa K / Miyata T / Makino F / Tanaka H / Namba K / Sowa K
History
DepositionSep 27, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61725.png

Downloads & links

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Map

FileDownload / File: emd_61725.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.0077624 - 3.351777
Average (Standard dev.)-0.00038134438 (±0.049778115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61725_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61725_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61725_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : D-fructose dehydrogenase Variant from Gluconobacter japonicus Tru...

EntireName: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions
Components
  • Complex: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions
    • Protein or peptide: Fructose dehydrogenase large subunit
    • Protein or peptide: Fructose dehydrogenase small subunit
    • Protein or peptide: Fructose dehydrogenase cytochrome subunit
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: HEME C

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Supramolecule #1: D-fructose dehydrogenase Variant from Gluconobacter japonicus Tru...

SupramoleculeName: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Fructose dehydrogenase large subunit

MacromoleculeName: Fructose dehydrogenase large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ec: 1.1.99.11
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 59.798309 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MSNETLSADV VIIGAGICGS LLAHKLVRNG LSVLLLDAGP RRDRSQIVEN WRNMPPDNKS QYDYATPYPS VPWAPHTNYF PDNNYLIVK GPDRTAYKQG IIKGVGGTTW HWAASSWRYL PNDFKLHSTY GVGRDYAMSY DELEPYYYEA ECEMGVMGPN G EEITPSAP ...String:
MSNETLSADV VIIGAGICGS LLAHKLVRNG LSVLLLDAGP RRDRSQIVEN WRNMPPDNKS QYDYATPYPS VPWAPHTNYF PDNNYLIVK GPDRTAYKQG IIKGVGGTTW HWAASSWRYL PNDFKLHSTY GVGRDYAMSY DELEPYYYEA ECEMGVMGPN G EEITPSAP RQNPWPMTSM PYGYGDRTFT EIVSKLGFSN TPVPQARNSR PYDGRPQCCG NNNCMPICPI GAMYNGVYAA IK AEKLGAK IIPNAVVYAM ETDAKNRITA ISFYDPDKQS HRVVAKTFVI AANGIETPKL LLLAANDRNP HGIANSSDLV GRN MMDHPG IGMSFQSAEP IWAGGGSVQM SSITNFRDGD FRSEYAATQI GYNNTAQNSR AGMKALSMGL VGKKLDEEIR RRTA HGVDI YANHEVLPDP NNRLVLSKDY KDALGIPHPE VTYDVGEYVR KSAAISRQRL MDIAKAMGGT EIEMTPYFTP NNHIT GGTI MGHDPRDSVV DKWLRTHDHS NLFLATGATM AASGTVNSTL TMAALSLRAA DAILNDLKQG

UniProtKB: Fructose dehydrogenase large subunit

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Macromolecule #2: Fructose dehydrogenase small subunit

MacromoleculeName: Fructose dehydrogenase small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 20.106732 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString:
MEKIADSGPV QIFLSRRKLL AFSGASLTVA AIGAPSKGST QDVVASNRDS ISDFMQLSAF ATGHKNLDLN IGSALLLAFE AQKHDFSTQ IKALREHITK NNYQDVEALD AAMKDDPLHP TLIQIIRAWY SGVIEDETNA KVYAFEKALM YQPSRDVVVI P TYAHNGPN YWVSEPASVD VMPAF

UniProtKB: Fructose dehydrogenase small subunit

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Macromolecule #3: Fructose dehydrogenase cytochrome subunit

MacromoleculeName: Fructose dehydrogenase cytochrome subunit / type: protein_or_peptide / ID: 3 / Details: deltaP27-I169 deltaG454-W476 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 34.431387 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MRYFRPLSAT AMTTVLLLAG TNVRAQAARI EGKPYVFDHT HNDDWNRGRY LVDELAHCGE CHTPRNFLLA PNQSAYLAGA DIGSWRAPN ITNAPQSGIG SWSDQDLFQY LKTGKTAHAR AAGPMAEAIE HSLQYLPDAD ISAIVTYLRS VPAKAESGQT V ANFEHAGR ...String:
MRYFRPLSAT AMTTVLLLAG TNVRAQAARI EGKPYVFDHT HNDDWNRGRY LVDELAHCGE CHTPRNFLLA PNQSAYLAGA DIGSWRAPN ITNAPQSGIG SWSDQDLFQY LKTGKTAHAR AAGPMAEAIE HSLQYLPDAD ISAIVTYLRS VPAKAESGQT V ANFEHAGR PSSYSVANAN SRRSNSTLTK TTDGAALYEA VCASCHQSDG KGSKDGYYPS LVGNTTTGQL NPNDLIASIL YG VDRTTDN HEILMPAFGP DSLVQPLTDE QIATIADYVL SHFGNAQATV SADAVKQVRA GGKQVPLAKL ASPLISRRKK RSA

UniProtKB: Fructose dehydrogenase cytochrome subunit, Fructose dehydrogenase cytochrome subunit

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #5: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #6: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
88.0 mmol/LNaH2PO4Sodium dihydrogen phosphate
12.0 mmol/LNa2HPO4Sodium hydrogen phosphate
9.0 mg/mLC14H28O6n-Octylglucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 500 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.01 mrad
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 20066 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 56754 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 7016675
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: 3D initial model from cryoSPARC ver. 4.2.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 1703212
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9jqa:
Cryo-EM Structure of Fructose Dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-Terminal Hydrophobic Regions

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