9JQA | pdb_00009jqa

Cryo-EM Structure of Fructose Dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-Terminal Hydrophobic Regions

• PDB DOI: https://doi.org/10.2210/pdb9JQA/pdb
• EM Map EMD-61725: EMDB EMDataResource

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


• Deposited: 2024-09-27 Released: 2025-08-06 
• Deposition Author(s): Adachi, T., Ichikawa, K., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1c and C-Terminal Hydrophobic Regions

Adachi, T., Ichikawa, K., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K.

(2025) Acs Electrochem 

• DOI: https://doi.org/10.1021/acselectrochem.5c00106

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 116.65 kDa 
• Atom Count: 7,431 
• Modeled Residue Count: 946 
• Deposited Residue Count: 1,047 
• Unique protein chains: 3

Macromolecules

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 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase cytochrome subunit	C	320	Gluconobacter japonicus	Mutation(s): 0  Gene Names: fdhC
UniProt
Find proteins for M1V1V5 (Gluconobacter japonicus) Explore M1V1V5  Go to UniProtKB:  M1V1V5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEC	F [auth C], G [auth C]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
F3S	E [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.2.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Adachi, T., Ichikawa, K., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121003
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K19281
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K14831

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release