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- PDB-8gy2: Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gl... -

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Basic information

Entry
Database: PDB / ID: 8gy2
TitleCryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gluconobacter oxydans
Components
  • (Alcohol dehydrogenase (quinone), ...) x 2
  • Small subunit of alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Complex / Oxidereductase / Membrane-bound protein
Function / homology
Function and homology information


alcohol dehydrogenase (quinone) / oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / electron transfer activity / iron ion binding / heme binding / calcium ion binding / plasma membrane
Similarity search - Function
Bacterial quinoprotein dehydrogenases signature 1. / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Cytochrome c, class IC / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / : / Pyrrolo-quinoline quinone repeat ...Bacterial quinoprotein dehydrogenases signature 1. / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Cytochrome c, class IC / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / : / Pyrrolo-quinoline quinone repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Cytochrome c / Quinoprotein alcohol dehydrogenase-like superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
HEME C / PYRROLOQUINOLINE QUINONE / UBIQUINONE-10 / Alcohol dehydrogenase (quinone), dehydrogenase subunit / Alcohol dehydrogenase, 15 kDa subunit / Alcohol dehydrogenase (quinone), cytochrome c subunit
Similarity search - Component
Biological speciesGluconobacter oxydans 621H (bacteria)
Gluconobacter oxydans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 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 1.0Aug 2, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 2, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase (quinone), dehydrogenase subunit
B: Alcohol dehydrogenase (quinone), cytochrome c subunit
C: Small subunit of alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,17810
Polymers148,4713
Non-polymers3,7087
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Alcohol dehydrogenase (quinone), ... , 2 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase (quinone), dehydrogenase subunit / ADH / Alcohol dehydrogenase (quinone) / acceptor subunit / subunit I / Ethanol:Q2 reductase / G3- ...ADH / Alcohol dehydrogenase (quinone) / acceptor subunit / subunit I / Ethanol:Q2 reductase / G3-ADH subunit I / Quinohemoprotein alcohol dehydrogenase / Quinohemoprotein-cytochrome c complex / Ubiquinol oxidase


Mass: 82938.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans 621H (bacteria) / Strain: 621H / Gene: adhA, GOX1068 / Production host: Gluconobacter oxydans (bacteria)
References: UniProt: O05542, alcohol dehydrogenase (quinone)
#2: Protein Alcohol dehydrogenase (quinone), cytochrome c subunit / ADH / Alcohol dehydrogenase (quinone) / subunit II / Cytochrome c-553 / Cytochrome c553 / Ethanol: ...ADH / Alcohol dehydrogenase (quinone) / subunit II / Cytochrome c-553 / Cytochrome c553 / Ethanol:Q2 reductase / G3-ADH subunit II / Quinohemoprotein-cytochrome c complex / Ubiquinol oxidase


Mass: 51249.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans 621H (bacteria) / Strain: 621H / Gene: adhB, GOX1067 / Production host: Gluconobacter oxydans (bacteria)
References: UniProt: Q47945, alcohol dehydrogenase (quinone)

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Protein , 1 types, 1 molecules C

#3: Protein Small subunit of alcohol dehydrogenase


Mass: 14282.063 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: O05544, alcohol dehydrogenase (quinone)

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Non-polymers , 4 types, 7 molecules

#4: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4

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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: Alcohol 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
30.6 mmol / L2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanolC14H22O(C2H4O)n1
41 mmol / LEthanolC2H6O1
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: 3224
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: 2551393
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247480 / 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_d0.00210257
ELECTRON MICROSCOPYf_angle_d0.54314033
ELECTRON MICROSCOPYf_dihedral_angle_d7.9571484
ELECTRON MICROSCOPYf_chiral_restr0.0431412
ELECTRON MICROSCOPYf_plane_restr0.0041829

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