8JEK | pdb_00008jek

Cryo-EM Structure of K-ferricyanide Oxidized Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus

PDB DOI: https://doi.org/10.2210/pdb8JEK/pdb
EM Map EMD-36191: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Gluconobacter japonicus
Expression System: Gluconobacter oxydans
Mutation(s): No

Deposited: 2023-05-16 Released: 2023-10-25
Deposition Author(s): Suzuki, Y., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry.

Suzuki, Y., Makino, F., Miyata, T., Tanaka, H., Namba, K., Kano, K., Sowa, K., Kitazumi, Y., Shirai, O.

(2023) ACS Catal 13

DOI: https://doi.org/10.1021/acscatal.3c03769

Macromolecule Content

Total Structure Weight: 135.96 kDa
Atom Count: 8,623
Modeled Residue Count: 1,089
Deposited Residue Count: 1,213
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase large subunit	A	544	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhL EC: 1.1.99.11 (PDB Primary Data), 1.1.5.14 (UniProt)
UniProt
Find proteins for M1VMF7 (Gluconobacter japonicus) Explore M1VMF7 Go to UniProtKB: M1VMF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1VMF7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase small subunit	B	183	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhS
UniProt
Find proteins for M1VB40 (Gluconobacter japonicus) Explore M1VB40 Go to UniProtKB: M1VB40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1VB40
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase cytochrome subunit	C	486	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhC
UniProt
Find proteins for M1V1V5 (Gluconobacter japonicus) Explore M1V1V5 Go to UniProtKB: M1V1V5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1V1V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth C]	F [auth C], G [auth C], H [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121003
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H01961
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K14831

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2025-09-17
Changes: Advisory, Data collection, Derived calculations, Structure summary