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- PDB-8gy3: Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from G... -

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Basic information

Entry
Database: PDB / ID: 8gy3
TitleCryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans
Components
  • Cytochrome c subunit of aldehyde dehydrogenase
  • Large subunit of aldehyde dehydrogenase
  • Small subunit of aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Complex / 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 / membrane / metal ion binding
Similarity search - Function
Oxidoreductase molybdopterin-binding subunit, IorB-related / : / : / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / 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 ...Oxidoreductase molybdopterin-binding subunit, IorB-related / : / : / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / 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 / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-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 / Cytochrome c family profile. / Cytochrome c-like domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Cytochrome c-like domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / Chem-PCD / UBIQUINONE-10 / CO/xanthine dehydrogenase Mo-binding subunit / Isoquinoline 1-oxidoreductase alpha subunit / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodELECTRON MICROSCOPY / single 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, 2items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c subunit of aldehyde dehydrogenase
B: Small subunit of aldehyde dehydrogenase
C: Large subunit of aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,53710
Polymers148,6223
Non-polymers3,9157
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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Protein , 3 types, 3 molecules ABC

#1: Protein Cytochrome c subunit of aldehyde dehydrogenase


Mass: 48519.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Production host: Gluconobacter oxydans (bacteria)
References: UniProt: Q5DW50, aldehyde dehydrogenase (FAD-independent)
#2: Protein Small subunit of aldehyde dehydrogenase


Mass: 16799.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Production host: Gluconobacter oxydans (bacteria)
References: UniProt: A0A4R4A2K3, aldehyde dehydrogenase (FAD-independent)
#3: Protein Large subunit of aldehyde dehydrogenase


Mass: 83302.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Production host: Gluconobacter oxydans (bacteria)
References: UniProt: A0A4R4A2F9, aldehyde dehydrogenase (FAD-independent)

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Non-polymers , 4 types, 7 molecules

#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-PCD / (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / MOLYBDENUM COFACTOR / MOCO


Mass: 844.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26MoN8O16P2S2

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Details

Has ligand of interestN
Has protein modificationY

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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: Aldehyde dehydrogenase from Gluconobacter oxydans / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: YES
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Source (recombinant)Organism: Gluconobacter oxydans (bacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
188 mmol / LSodium dihydrogen phosphateNaH2PO41
212 mmol / LSodium hydrogen phosphateNa2HPO41
30.3 mmol / L2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanolC14H22O(C2H4O)n1
41 mmol / LAcetaldehydeC2H4O1
SpecimenConc.: 10 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 50 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: 12747
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
2SerialEM3.9image acquisition
4cryoSPARC3.3.2CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6871333
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189414 / 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_d0.00310597
ELECTRON MICROSCOPYf_angle_d0.55914489
ELECTRON MICROSCOPYf_dihedral_angle_d8.881554
ELECTRON MICROSCOPYf_chiral_restr0.0431554
ELECTRON MICROSCOPYf_plane_restr0.0041882

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