7W2J

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

• PDB DOI:  https://doi.org/10.2210/pdb7W2J/pdb
• EM Map EMD-32262: EMDB EMDataResource

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


• Deposited: 2021-11-24 Released: 2022-11-30 
• Deposition Author(s): Suzuki, Y., Makino, F., Miyata, T., 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and Bioelectrochemical Elucidation of Direct Electron Transfer-type Membrane-bound Fructose Dehydrogenase

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 270.19 kDa 
• Atom Count: 16,522 
• Modelled Residue Count: 2,104 
• Deposited Residue Count: 2,426 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase large subunit	A, D	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, E	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, F	486	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 (Subject of Investigation/LOI)	G [auth A], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEC (Subject of Investigation/LOI)	I [auth C], J [auth C], K [auth C], N [auth F], O [auth F], P [auth F]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
F3S	H [auth A], M [auth D]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Suzuki, Y., Makino, F., Miyata, T., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101117
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H01961

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references