[English] 日本語
Yorodumi
- EMDB-34368: Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34368
TitleCryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gluconobacter oxydans
Map data
Sample
  • Complex: Alcohol dehydrogenase from Gluconobacter oxydans
    • Protein or peptide: Alcohol dehydrogenase (quinone), dehydrogenase subunitAlcohol dehydrogenase (quinone)
    • Protein or peptide: Alcohol dehydrogenase (quinone), cytochrome c subunitAlcohol dehydrogenase (quinone)
    • Protein or peptide: Small subunit of alcohol dehydrogenase
  • Ligand: HEME C
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: CALCIUM IONCalcium
  • Ligand: UBIQUINONE-10Coenzyme Q10
KeywordsComplex / Oxidereductase / Membrane-bound protein / OXIDOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase (quinone) / oxidoreductase activity, acting on CH-OH group of donors / respirasome / outer membrane-bounded periplasmic space / electron transfer activity / iron ion binding / calcium ion binding / heme binding / plasma membrane
Similarity search - Function
Bacterial quinoprotein dehydrogenases signature 1. / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Cytochrome c, class IC / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat ...Bacterial quinoprotein dehydrogenases signature 1. / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Cytochrome c, class IC / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Cytochrome C oxidase, cbb3-type, subunit III / 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) / Gluconobacter oxydans 621H (bacteria)
Methodsingle 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, 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

-
Structure visualization

Supplemental images

emd_34368.png

Downloads & links

-
Map

FileDownload / File: emd_34368.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: 0.16
Minimum - Maximum-0.24867207 - 0.62730235
Average (Standard dev.)0.00080129766 (±0.0165849)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34368_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34368_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34368_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Alcohol dehydrogenase from Gluconobacter oxydans

EntireName: Alcohol dehydrogenase from Gluconobacter oxydans
Components
  • Complex: Alcohol dehydrogenase from Gluconobacter oxydans
    • Protein or peptide: Alcohol dehydrogenase (quinone), dehydrogenase subunitAlcohol dehydrogenase (quinone)
    • Protein or peptide: Alcohol dehydrogenase (quinone), cytochrome c subunitAlcohol dehydrogenase (quinone)
    • Protein or peptide: Small subunit of alcohol dehydrogenase
  • Ligand: HEME C
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: CALCIUM IONCalcium
  • Ligand: UBIQUINONE-10Coenzyme Q10

-
Supramolecule #1: Alcohol dehydrogenase from Gluconobacter oxydans

SupramoleculeName: Alcohol dehydrogenase from Gluconobacter oxydans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gluconobacter oxydans (bacteria)
Molecular weightTheoretical: 150 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 621H (bacteria) / Strain: 621H
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 621H (bacteria) / Strain: 621H
Molecular weightTheoretical: 51.249598 KDa
Recombinant expressionOrganism: Gluconobacter oxydans (bacteria)
SequenceString: MLNALTRDRL VSEMKQGWKL AAAIGLMAVS FGAAHAQDAD EALIKRGEYV ARLSDCIACH TALHGQPYAG GLEIKSPIGT IYSTNITPD PEHGIGNYTL EDFTKALRKG IRKDGATVYP AMPYPEFARL SDDDIRAMYA FFMHGVKPVA LQNKAPDISW P LSMRWPLG ...String:
MLNALTRDRL VSEMKQGWKL AAAIGLMAVS FGAAHAQDAD EALIKRGEYV ARLSDCIACH TALHGQPYAG GLEIKSPIGT IYSTNITPD PEHGIGNYTL EDFTKALRKG IRKDGATVYP AMPYPEFARL SDDDIRAMYA FFMHGVKPVA LQNKAPDISW P LSMRWPLG MWRAMFVPSM TPGVDKSISD PEVARGEYLV NGPGHCGECH TPRGFGMQVK AYGTAGGNAY LAGGAPIDNW IA PSLRSNS DTGLGRWSED DIVTFLKSGR IDHSAVFGGM ADVVAYSTQH WSDDDLRATA KYLKSMPAVP EGKNLGQDDG QTT ALLNKG GQGNAGAEVY LHNCAICHMN DGTGVNRMFP PLAGNPVVIT DDPTSLANVV AFGGILPPTN SAPSAVAMPG FKNH LSDQE MADVVNFMRK GWGNNAPGTV SASDIQKLRT TGAPVSTAGW NVSSKGWMAY MPQPYGEDWT FSPQTHTGVD DAQ

UniProtKB: 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: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / 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 / Pyrroloquinoline quinone

-
Macromolecule #6: CALCIUM ION

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

-
Macromolecule #7: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 7 / Number of copies: 1 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
88.0 mmol / LNaH2PO4Sodium dihydrogen phosphate
12.0 mmol / LNa2HPO4Sodium hydrogen phosphate
0.6 mmol / LC14H22O(C2H4O)n2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanol
1.0 mmol / LC2H6OEthanol
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

-
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: 3224 / Average exposure time: 3.0 sec. / Average electron dose: 2.0 e/Å2

-
Image processing

Particle selectionNumber selected: 2551393
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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 247480
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8gy2:
Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gluconobacter oxydans

+
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