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- EMDB-36190: Cryo-EM Structure of Na-dithionite Reduced Membrane-bound Fructos... -

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Basic information

Entry
Database: EMDB / ID: EMD-36190
TitleCryo-EM Structure of Na-dithionite Reduced Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus
Map data
Sample
  • Complex: D-fructose dehydrogenase from Gluconobacter japonicus
    • Protein or peptide: Fructose dehydrogenase large subunit
    • Protein or peptide: Fructose dehydrogenase small subunit
    • Protein or peptide: Fructose dehydrogenase cytochrome subunit
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: FE3-S4 CLUSTER
  • Ligand: HEME C
  • Ligand: UBIQUINONE-10Coenzyme Q10
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 / 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
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: 2.5 Å
AuthorsSuzuki Y / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O
Funding support Japan, 3 items
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, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36190.png

Downloads & links

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Map

FileDownload / File: emd_36190.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3328694 - 2.3449595
Average (Standard dev.)0.0024967582 (±0.047301244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 243.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D-fructose dehydrogenase from Gluconobacter japonicus

EntireName: D-fructose dehydrogenase from Gluconobacter japonicus
Components
  • Complex: D-fructose dehydrogenase from Gluconobacter japonicus
    • Protein or peptide: Fructose dehydrogenase large subunit
    • Protein or peptide: Fructose dehydrogenase small subunit
    • Protein or peptide: Fructose dehydrogenase cytochrome subunit
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: FE3-S4 CLUSTER
  • Ligand: HEME C
  • Ligand: UBIQUINONE-10Coenzyme Q10

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Supramolecule #1: D-fructose dehydrogenase from Gluconobacter japonicus

SupramoleculeName: D-fructose dehydrogenase from Gluconobacter japonicus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 140 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Molecular weightTheoretical: 52.252652 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MRYFRPLSAT AMTTVLLLAG TNVRAQPTEP TPASAHRPSI SRGHYLAIAA DCAACHTNGR DGQFLAGGYA ISSPMGNIYS TNITPSKTH GIGNYTLEQF SKALRHGIRA DGAQLYPAMP YDAYNRLTDE DVKSLYAYIM TEVKPVDAPS PKTQLPFPFS I RASLGIWK ...String:
MRYFRPLSAT AMTTVLLLAG TNVRAQPTEP TPASAHRPSI SRGHYLAIAA DCAACHTNGR DGQFLAGGYA ISSPMGNIYS TNITPSKTH GIGNYTLEQF SKALRHGIRA DGAQLYPAMP YDAYNRLTDE DVKSLYAYIM TEVKPVDAPS PKTQLPFPFS I RASLGIWK IAARIEGKPY VFDHTHNDDW NRGRYLVDEL AHCGECHTPR NFLLAPNQSA YLAGADIGSW RAPNITNAPQ SG IGSWSDQ DLFQYLKTGK TAHARAAGPM AEAIEHSLQY LPDADISAIV TYLRSVPAKA ESGQTVANFE HAGRPSSYSV ANA NSRRSN STLTKTTDGA ALYEAVCASC HQSDGKGSKD GYYPSLVGNT TTGQLNPNDL IASILYGVDR TTDNHEILMP AFGP DSLVQ PLTDEQIATI ADYVLSHFGN AQATVSADAV KQVRAGGKQV PLAKLASPGV MLLLGTGGIL GAILVVAGLW WLISR RKKR SA

UniProtKB: 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 / Flavin adenine dinucleotide

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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 / Iron–sulfur cluster

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Macromolecule #6: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 6 / Number of copies: 3 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #7: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 7 / Number of copies: 1 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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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
176.0 mmol / LNaH2PO4Sodium dihydrogen phosphate
24.0 mmol / LNa2HPO4Sodium hydrogen phosphate
1.5 mmol / LC14H22O(C2H4O)n2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanol
1.0 mmol / LC2H6OS2-Mercaptoethanol
1.0 mmol / LNa2S2O4Sodium dithionite
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. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.01 mrad
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4500 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2

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Image processing

Particle selectionNumber selected: 1013610
Startup modelType of model: OTHER / Details: 3D initial model from cryoSPARC ver. 3.3.2
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 315288

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8jej:
Cryo-EM Structure of Na-dithionite Reduced Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus

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