[English] 日本語
Yorodumi
- PDB-7w2j: Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w2j
TitleCryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus
Components(Fructose dehydrogenase ...) x 3
KeywordsOXIDOREDUCTASE / Complex / OXIDOREDUCTASE Membrane-bound protein
Function / homology
Function and homology information


fructose 5-dehydrogenase / fructose 5-dehydrogenase activity / oxidoreductase activity, acting on CH-OH group of donors / fructose metabolic process / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / : / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase ...FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / : / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / HEME C / Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase small subunit / Fructose dehydrogenase large subunit
Similarity search - Component
Biological speciesGluconobacter japonicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSuzuki, Y. / Makino, F. / Miyata, T. / Tanaka, H. / Namba, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01961 Japan
CitationJournal: Acs Catalysis / Year: 2023
Title: Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry
Authors: Suzuki, Y. / Makino, F. / Miyata, T. / Tanaka, H. / Namba, K. / Kano, K. / Sowa, K. / Kitazumi, Y. / Shirai, O.
History
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose dehydrogenase large subunit
B: Fructose dehydrogenase small subunit
C: Fructose dehydrogenase cytochrome subunit
D: Fructose dehydrogenase large subunit
E: Fructose dehydrogenase small subunit
F: Fructose dehydrogenase cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,18916
Polymers264,3156
Non-polymers5,87410
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Fructose dehydrogenase ... , 3 types, 6 molecules ADBECF

#1: Protein Fructose dehydrogenase large subunit / Fructose dehydrogenase subunit I


Mass: 59798.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhL / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1VMF7, EC: 1.1.99.11
#2: Protein Fructose dehydrogenase small subunit / Fructose dehydrogenase subunit III


Mass: 20106.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhS / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1VB40
#3: Protein Fructose dehydrogenase cytochrome subunit / Fructose dehydrogenase subunit II


Mass: 52252.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter japonicus (bacteria) / Gene: fdhC / Production host: Gluconobacter oxydans (bacteria) / References: UniProt: M1V1V5

-
Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#6: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: D-fructose dehydrogenase from Gluconobacter japonicus / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: YES
Source (natural)Organism: Gluconobacter japonicus (bacteria)
Source (recombinant)Organism: Gluconobacter oxydans (bacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
1176 mmol / LSodium dihydrogen phosphateNaH2PO41
224 mmol / LSodium hydrogen phosphateNa2HPO41
31.5 mmol / L2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanolC14H22O(C2H4O)n1
41 mmol / L2-MercaptoethanolC2H6OS1
SpecimenConc.: 5 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
VitrificationCryogen name: ETHANE

-
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: 40 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: 5575
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1Warp1.09particle selection
2SerialEM3.9image acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 365385
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91745 / 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_d0.00916972
ELECTRON MICROSCOPYf_angle_d0.97223202
ELECTRON MICROSCOPYf_dihedral_angle_d8.9732346
ELECTRON MICROSCOPYf_chiral_restr0.0532476
ELECTRON MICROSCOPYf_plane_restr0.0062986

+
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