[English] 日本語
Yorodumi
- EMDB-66440: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66440
TitleCryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 2)
Map data
Sample
  • Complex: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Bound Regions (Form 2)
    • Protein or peptide: Alcohol dehydrogenase (quinone), dehydrogenase subunit
    • Protein or peptide: Alcohol dehydrogenase (quinone), cytochrome c subunit
    • Protein or peptide: Small subunit of alcohol dehydrogenase
  • Ligand: HEME C
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: CALCIUM ION
KeywordsComples / Oxidoreductase / 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
Alcohol dehydrogenase (quinone), dehydrogenase subunit / Alcohol dehydrogenase, 15 kDa subunit / Alcohol dehydrogenase (quinone), cytochrome c subunit
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
Methodsingle 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, 3 items
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, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66440.png

Downloads & links

-
Map

FileDownload / File: emd_66440.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 274.88 Å		0.86 Å/pix.
x 320 pix.
= 274.88 Å		0.86 Å/pix.
x 320 pix.
= 274.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.09123922 - 0.23958996
Average (Standard dev.)0.00020070659 (±0.005906535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 274.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66440_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66440_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66440_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconoba...

EntireName: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Bound Regions (Form 2)
Components
  • Complex: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Bound Regions (Form 2)
    • Protein or peptide: Alcohol dehydrogenase (quinone), dehydrogenase subunit
    • Protein or peptide: Alcohol dehydrogenase (quinone), cytochrome c subunit
    • Protein or peptide: Small subunit of alcohol dehydrogenase
  • Ligand: HEME C
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: CALCIUM ION

-
Supramolecule #1: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconoba...

SupramoleculeName: Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Bound Regions (Form 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 140 KDa

-
Macromolecule #1: Alcohol dehydrogenase (quinone), dehydrogenase subunit

MacromoleculeName: Alcohol dehydrogenase (quinone), dehydrogenase subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: alcohol dehydrogenase (quinone)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 82.938906 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MTSGLLTPIK VTKKRLLSCA AALAFSAAVP VAFAQEDTGT AITSSDNGGH PGDWLSYGRS YSEQRYSPLD QINTENVGKL KLAWHYDLD TNRGQEGTPL IVNGVMYATT NWSKMKALDA ATGKLLWSYD PKVPGNIADR GCCDTVSRGA AYWNGKVYFG T FDGRLIAL ...String:
MTSGLLTPIK VTKKRLLSCA AALAFSAAVP VAFAQEDTGT AITSSDNGGH PGDWLSYGRS YSEQRYSPLD QINTENVGKL KLAWHYDLD TNRGQEGTPL IVNGVMYATT NWSKMKALDA ATGKLLWSYD PKVPGNIADR GCCDTVSRGA AYWNGKVYFG T FDGRLIAL DAKTGKLVWS VYTIPKEAQL GHQRSYTVDG APRIAKGKVL IGNGGAEFGA RGFVSAFDAE TGKLDWRFFT VP NPENKPD GAASDDILMS KAYPTWGKNG AWKQQGGGGT VWDSLVYDPV TDLVYLGVGN GSPWNYKFRS EGKGDNLFLG SIV AINPDT GKYVWHFQET PMDEWDYTSV QQIMTLDMPV NGEMRHVIVH APKNGFFYII DAKTGKFITG KPYTYENWAN GLDP VTGRP NYVPDALWTL TGKPWLGIPG ELGGHNFAAM AYSPKTKLVY IPAQQIPLLY DGQKGGFKAY HDAWNLGLDM NKIGL FDDN DPEHVAAKKD FLKVLKGWTV AWDPEKMAPA FTINHKGPWN GGLLATAGNV IFQGLANGEF HAYDATNGND LYSFPA QSA IIAPPVTYTA NGKQYVAVEV GWGGIYPFLY GGVARTSGWT VNHSRVIAFS LDGKDSLPPK NELGFTPVKP VPTYDEA RQ KDGYFMYQTF CSACHGDNAI SGGVLPDLRW SGAPRGRESF YKLVGRGALT AYGMDRFDTS MTPEQIEDIR NFIVKRAN E SYDDEVKARE NSTGVPNDQF LNVPQSTADV PTADHP

UniProtKB: Alcohol dehydrogenase (quinone), dehydrogenase subunit

-
Macromolecule #2: Alcohol dehydrogenase (quinone), cytochrome c subunit

MacromoleculeName: Alcohol dehydrogenase (quinone), cytochrome c subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: alcohol dehydrogenase (quinone)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 48.939645 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MLNALTRDRL VSEMKQGWKL AAAIGLMAVS FGAAHAQDAD EALIKRGEYV ARLSDCIACH TALHGQPYAG GLEIKSGGGT IYSTNITPD PEHGIGNYTL EDFTKALRKG IRKDGATVYP AMPYPEFARL SDDDIRAMYA FFMHGVKPVA LQNKAPDISG G GGVPSMTP ...String:
MLNALTRDRL VSEMKQGWKL AAAIGLMAVS FGAAHAQDAD EALIKRGEYV ARLSDCIACH TALHGQPYAG GLEIKSGGGT IYSTNITPD PEHGIGNYTL EDFTKALRKG IRKDGATVYP AMPYPEFARL SDDDIRAMYA FFMHGVKPVA LQNKAPDISG G GGVPSMTP GVDKSISDPE VARGEYLVNG PGHCGECHTP RQVKAYGTAG GNAYLAGGAP IDNWIAPSLR SNSDTGLGRW SE DDIVTFL KSGRIDHSAV FGGMADVVAY STQHWSDDDL RATAKYLKSM PAVPEGKNLG QDDGQTTALL NKGGQGNAGA EVY LHNCAI CHMNDGTGVN RMFPPLAGNP VVITDDPTSL ANVVAFGGIL PPTNSAPSAV AMPGFKNHLS DQEMADVVNF MRKG WGNNA PGTVSASDIQ KLRTTGAPVS TAGWNVSSKG WMAYMPQPYG EDWTFSPQTH TGVDDAQ

UniProtKB: Alcohol dehydrogenase (quinone), cytochrome c subunit, Alcohol dehydrogenase (quinone), cytochrome c subunit

-
Macromolecule #3: Small subunit of alcohol dehydrogenase

MacromoleculeName: Small subunit of alcohol dehydrogenase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: alcohol dehydrogenase (quinone)
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 14.282063 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString:
MFRRIVPVLG LALGLGLASQ AAMAQEQSPP PPPAVQGTPG KDFTGVSPAN LAGIMNYCVE QQYVSYDEGN PVLYGLSEKY KATEQTVGN FDYALGTAGY FDSNGKRFYL VAYTNEDDRR AACHAAVKAA QPML

UniProtKB: Alcohol dehydrogenase, 15 kDa subunit

-
Macromolecule #4: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 4 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 620.519 Da
Chemical component information

ChemComp-HEC:
HEME C

-
Macromolecule #5: PYRROLOQUINOLINE QUINONE

MacromoleculeName: PYRROLOQUINOLINE QUINONE / type: ligand / ID: 5 / Number of copies: 1 / Formula: PQQ
Molecular weightTheoretical: 330.206 Da
Chemical component information

ChemComp-PQQ:
PYRROLOQUINOLINE QUINONE

-
Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
141.0 mmol/LKH2PO4Potassium dihydrogen phosphate
19.0 mmol/LK2HPO4Dipotassium hydrogen phosphate
9.0 mg/mLC14H28O6n-Octylglucoside
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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
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: 20066 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2
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 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

+
Image processing

Particle selectionNumber selected: 10399280
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: 3D Initial model from cryoSPARC ver. 4.2.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 119667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9x0r:
Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 2)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more