8JEK

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

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 1.0 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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose dehydrogenase large subunit544Gluconobacter japonicusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VMF7
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose dehydrogenase small subunit183Gluconobacter japonicusMutation(s): 0 
Gene Names: fdhS
UniProt
Find proteins for M1VB40 (Gluconobacter japonicus)
Explore M1VB40 
Go to UniProtKB:  M1VB40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VB40
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose dehydrogenase cytochrome subunit486Gluconobacter japonicusMutation(s): 0 
Gene Names: fdhC
UniProt
Find proteins for M1V1V5 (Gluconobacter japonicus)
Explore M1V1V5 
Go to UniProtKB:  M1V1V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1V1V5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U10 (Subject of Investigation/LOI)
Query on U10
Download Ideal Coordinates CCD File 
I [auth C]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
FAD (Subject of Investigation/LOI)
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEC (Subject of Investigation/LOI)
Query on HEC
Download Ideal Coordinates CCD File 
F [auth C],
G [auth C],
H [auth C]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
F3S
Query on F3S
Download Ideal Coordinates CCD File 
E [auth A]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121003
Japan Society for the Promotion of Science (JSPS)JapanJP21H01961
Japan Society for the Promotion of Science (JSPS)JapanJP22K14831

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release