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- EMDB-34369: Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from G... -

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Basic information

Entry
Database: EMDB / ID: EMD-34369
TitleCryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans
Map data
Sample
  • Complex: Aldehyde dehydrogenase from Gluconobacter oxydans
    • Protein or peptide: Cytochrome c subunit of aldehyde dehydrogenase
    • Protein or peptide: Small subunit of aldehyde dehydrogenase
    • Protein or peptide: Large subunit of aldehyde dehydrogenase
  • Ligand: HEME C
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
KeywordsComplex / Oxidoreductase / Membrane-bound protein
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Oxidoreductase molybdopterin-binding subunit, IorB-related / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily ...Oxidoreductase molybdopterin-binding subunit, IorB-related / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Cytochrome C oxidase, cbb3-type, subunit III / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome c / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Cytochrome c family profile. / Cytochrome c-like domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
CO/xanthine dehydrogenase Mo-binding subunit / Isoquinoline 1-oxidoreductase alpha subunit / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsAdachi T / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01961 Japan
CitationJournal: Acs Catalysis / Year: 2023
Title: Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases
Authors: Adachi T / Miyata T / Makino F / Tanaka H / Namba K / Kano K / Sowa K / Kitazumi Y / Shirai O
History
DepositionSep 21, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34369.png

Downloads & links

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Map

FileDownload / File: emd_34369.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.23456362 - 0.66902375
Average (Standard dev.)0.00066653406 (±0.013812292)
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_34369_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34369_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_34369_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Aldehyde dehydrogenase from Gluconobacter oxydans

EntireName: Aldehyde dehydrogenase from Gluconobacter oxydans
Components
  • Complex: Aldehyde dehydrogenase from Gluconobacter oxydans
    • Protein or peptide: Cytochrome c subunit of aldehyde dehydrogenase
    • Protein or peptide: Small subunit of aldehyde dehydrogenase
    • Protein or peptide: Large subunit of aldehyde dehydrogenase
  • Ligand: HEME C
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)

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Supramolecule #1: Aldehyde dehydrogenase from Gluconobacter oxydans

SupramoleculeName: Aldehyde dehydrogenase from Gluconobacter oxydans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Cytochrome c subunit of aldehyde dehydrogenase

MacromoleculeName: Cytochrome c subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 48.5195 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MLKRIAAAVI GLGAVGGIGF LAYAWYPAIA PIPRPAASSF SADAISRGEI VANGGYCAEC HTRVDGKPGP ELAGDFKMAT PFGDIFSSN ITPDEEWGIG NWSLAAFKRA MNKGIARDGS QLYPAFPFDH FTKVSDQDVS DLYAYLMTRP AVHLKPRDNT V PFPINIRL ...String:
MLKRIAAAVI GLGAVGGIGF LAYAWYPAIA PIPRPAASSF SADAISRGEI VANGGYCAEC HTRVDGKPGP ELAGDFKMAT PFGDIFSSN ITPDEEWGIG NWSLAAFKRA MNKGIARDGS QLYPAFPFDH FTKVSDQDVS DLYAYLMTRP AVHLKPRDNT V PFPINIRL IGQGFWKLLF FTPGRYQNDP KHDAQWNRGA YLAEGNEHCG ACHTPRNLLG AEKMSSVYDG AVIDGWIAPP LN DHNPTPV VWTEDELFQY LRFGVAPLHG SAAGPMSPVP HRFLSKIPEE DVHAIAHYYA DVDKAAQRSS GDQAAITRAM QMS GRDLTG PQPLDEDARL YQGACGACHY NSGPNPVLGR PELALNNALW LDEPNNLYQV MLHGITAEEG QDHISMPSFY SGLS DHDMA RIAAYLRRTR TTLPPWTDLE KKAASARATL EAPPVNASH

UniProtKB: Aldehyde dehydrogenase

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Macromolecule #2: Small subunit of aldehyde dehydrogenase

MacromoleculeName: Small subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 16.799998 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString:
MTTKFELNGQ PVTVDAPADT PLLWVIRDDL NLTGTKFGCG IGECGACTVH VGGRATRSCI TPLSAVEGAS ITTIEGLDPA GNHVVQVAW RDQQVPQCGY CQSGQIMQAA SLLKDYPNPT DDQIDGVMGG SLCRCMTYIR IRKAIKEAAS RQQEGANNG

UniProtKB: Isoquinoline 1-oxidoreductase alpha subunit

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Macromolecule #3: Large subunit of aldehyde dehydrogenase

MacromoleculeName: Large subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 83.302164 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MAKIEQIAKK SDATRLSRRN FLMTAAGAGL MFGFARKAGA ATTLPSAMPP EAAFEPNIWC AIAPDGSINV NIVRAEMGQH VGTALARII ADEMDADWDK IKITQVDTAP KWAGKYVTGG SWSVWDTWDT FRQAGAAARS VMIEEGAKLL GTTPDRCTAH E SVVSAGSK ...String:
MAKIEQIAKK SDATRLSRRN FLMTAAGAGL MFGFARKAGA ATTLPSAMPP EAAFEPNIWC AIAPDGSINV NIVRAEMGQH VGTALARII ADEMDADWDK IKITQVDTAP KWAGKYVTGG SWSVWDTWDT FRQAGAAARS VMIEEGAKLL GTTPDRCTAH E SVVSAGSK SISFGDIVAR AKPTRTFTPE EMAKLPLKPT GNRRLISKQV PALDIPDKTT GKAIYGIDVK LDGMVYGRPK MP PTRYAAK VISVDDSAAK KIPGYLRYVV LDDPSGIVPG WVVALAKTYP AAIRAADALK VQWNPGPTIN VSEADIIEHG RKL AADPKN GTRVFNDKGV DEALTIHPGQ VFERSYTCAS VAHYQLEPVN AVARHIDGMW EIHTGNQWQS LILPQLAKSL QVPE EQVVM RTYMLGGGFG RRLNGDYCIP AALASKAIGG APVKLILTRS DDMELDSIRS PSIQTIKVAL DNDRKKIVGM DYVAV AGWP TQVMAPAFLA TGEDGKKYDP FAIAGADHWY ETGPTRVRAI SNDLANATFR PGWLRSVSAG WTPWALECFL DELAHS TKQ DPLAFRLSMF TAQGRNAGQA PNSVGGAKRQ AAVLQRLADK IGYANKQLPA DTGIGIATSF GQERGMPTWT AAAAQIH VD RKTGVVTCQK LWLVLDAGTI VDPGGALAQT EGAALWGFSM ALFEGTEIVN GTIKDRNLNT YTPLRIPDVP DIDIEFIQ N TEKPTGLGEP GVTVVAPAIG NAIFNAVGIR LRHMPMRPAD VRRELQQHTS

UniProtKB: CO/xanthine dehydrogenase Mo-binding subunit

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Macromolecule #4: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 4 / 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 #5: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 5 / Number of copies: 1 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #7: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)

MacromoleculeName: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
type: ligand / ID: 7 / Number of copies: 1 / Formula: PCD
Molecular weightTheoretical: 844.471 Da
Chemical component information

ChemComp-PCD:
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / Molybdenum cofactor

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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

Concentration10 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
88.0 mmol / LNaH2PO4Sodium dihydrogen phosphate
12.0 mmol / LNa2HPO4Sodium hydrogen phosphate
0.3 mmol / LC14H22O(C2H4O)n2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanol
1.0 mmol / LC2H4OAcetaldehyde
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 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
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: 12747 / Average exposure time: 3.0 sec. / Average electron dose: 2.0 e/Å2

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Image processing

Particle selectionNumber selected: 6871333
Startup modelType of model: OTHER / Details: 3D initial model from cryoSPARC 3.3.2
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 3 / Avg.num./class: 300000 / 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: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 189414
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8gy3:
Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans

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