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- PDB-9x0r: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconoba... -

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Basic information

Entry
Database: PDB / ID: 9x0r
TitleCryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 2)
Components
  • (Alcohol dehydrogenase (quinone), ...) x 2
  • Small subunit of alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Comples / Membrane-bound protein
Function / homology
Function and homology information


alcohol dehydrogenase (quinone) / oxidoreductase activity, acting on CH-OH group of donors / respiratory electron transport chain / 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 / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein dehydrogenase, conserved site / PQQ-dependent dehydrogenase, methanol/ethanol family / Cytochrome c, class IC / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / : / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat ...Bacterial quinoprotein dehydrogenases signature 1. / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein dehydrogenase, conserved site / PQQ-dependent dehydrogenase, methanol/ethanol family / Cytochrome c, class IC / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / : / Pyrrolo-quinoline quinone repeat / 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
Similarity search - Domain/homology
HEME C / PYRROLOQUINOLINE QUINONE / Alcohol dehydrogenase (quinone), dehydrogenase subunit / Alcohol dehydrogenase, 15 kDa subunit / Alcohol dehydrogenase (quinone), cytochrome c subunit
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsIchikawa, K. / Adachi, T. / Miyata, T. / Makino, F. / Namba, K. / Kitazumi, Y. / Shirai, O. / Sowa, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K19281 Japan
Japan Society for the Promotion of Science (JSPS)JP22K14831 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
CitationJournal: Chem Commun (Camb) / Year: 2026
Title: Structure-guided engineering of membrane-binding regions for surfactant-free solubilization of direct electron transfer-type alcohol dehydrogenase.
Authors: Konatsu Ichikawa / Taiki Adachi / Tomoko Miyata / Fumiaki Makino / Keiichi Namba / Yuki Kitazumi / Osamu Shirai / Keisei Sowa /
Abstract: Membrane-bound alcohol dehydrogenase (ADH) from is a direct electron transfer-type biocatalyst for ethanol oxidation. To improve its bioelectrocatalysis, membrane-binding regions of ADH were ...Membrane-bound alcohol dehydrogenase (ADH) from is a direct electron transfer-type biocatalyst for ethanol oxidation. To improve its bioelectrocatalysis, membrane-binding regions of ADH were predicted, resulting in the construction of a soluble ADH variant by enzyme engineering. The variant was purified and characterized using structural and bioelectrochemical approaches.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)149,0139
Polymers146,1613
Non-polymers2,8526
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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 (bacteria) / 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: 48939.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / 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 , 3 types, 6 molecules

#4: Chemical
ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Bound Regions (Form 2)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: YES
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Source (recombinant)Organism: Gluconobacter oxydans (bacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
1141 mmol/LPotassium dihydrogen phosphateKH2PO41
219 mmol/LDipotassium hydrogen phosphateK2HPO41
39 mg/mLn-OctylglucosideC14H28O61
SpecimenConc.: 3 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: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20066
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.0particle selection
2SerialEM3.9image acquisition
4cryoSPARC4.2.0CTF correction
7Cootmodel fitting
9cryoSPARC4.2.0initial Euler assignment
10cryoSPARC4.2.0final Euler assignment
11cryoSPARC4.2.0classification
12cryoSPARC4.2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10399280
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119667 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029252
ELECTRON MICROSCOPYf_angle_d0.52612670
ELECTRON MICROSCOPYf_dihedral_angle_d6.1971281
ELECTRON MICROSCOPYf_chiral_restr0.0431277
ELECTRON MICROSCOPYf_plane_restr0.0041650

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