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- EMDB-32764: Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from G... -

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Basic information

Entry
Database: EMDB / ID: EMD-32764
TitleCryo-EM Structure of 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 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: 3.8 Å
AuthorsSuzuki Y / Makino F
Funding support Japan, 2 items
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
DepositionFeb 1, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32764.png

Downloads & links

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Map

FileDownload / File: emd_32764.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 243.6 Å		0.87 Å/pix.
x 280 pix.
= 243.6 Å		0.87 Å/pix.
x 280 pix.
= 243.6 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: 0.01
Minimum - Maximum-0.06034248 - 0.13130799
Average (Standard dev.)0.00011442983 (±0.0031477772)
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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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 DINUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: HEME C

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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: 2 / 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: 2 / 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: 2 / 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: 2 / 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: 2 / 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: 6 / 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
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
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
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: 5575 / Average exposure time: 3.0 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 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: 365385
Startup modelType of model: OTHER / Details: 3D initial model from relion3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 140565
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 40000 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7wsq:
Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus

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