2GMH | pdb_00002gmh

Structure of Porcine Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase in Complexed with Ubiquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.254 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2GMH

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.

Zhang, J.Frerman, F.E.Kim, J.J.

(2006) Proc Natl Acad Sci U S A 103: 16212-16217

  • DOI: https://doi.org/10.1073/pnas.0604567103
  • Primary Citation Related Structures: 
    2GMH, 2GMJ

  • PubMed Abstract: 

    Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a 4Fe4S flavoprotein located in the inner mitochondrial membrane. It catalyzes ubiquinone (UQ) reduction by ETF, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. Deficiencies in ETF or ETF-QO result in multiple acyl-CoA dehydrogenase deficiency, a human metabolic disease. Crystal structures of ETF-QO with and without bound UQ were determined, and they are essentially identical. The molecule forms a single structural domain. Three functional regions bind FAD, the 4Fe4S cluster, and UQ and are closely packed and share structural elements, resulting in no discrete structural domains. The UQ-binding pocket consists mainly of hydrophobic residues, and UQ binding differs from that of other UQ-binding proteins. ETF-QO is a monotopic integral membrane protein. The putative membrane-binding surface contains an alpha-helix and a beta-hairpin, forming a hydrophobic plateau. The UQ-flavin distance (8.5 A) is shorter than the UQ-cluster distance (18.8 A), and the very similar redox potentials of FAD and the cluster strongly suggest that the flavin, not the cluster, transfers electrons to UQ. Two possible electron transfer paths can be envisioned. First, electrons from the ETF flavin semiquinone may enter the ETF-QO flavin one by one, followed by rapid equilibration with the cluster. Alternatively, electrons may enter via the cluster, followed by equilibration between centers. In both cases, when ETF-QO is reduced to a two-electron reduced state (one electron at each redox center), the enzyme is primed to reduce UQ to ubiquinol via FAD.


  • Organizational Affiliation
    • Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

Macromolecule Content 

  • Total Structure Weight: 134.61 kDa 
  • Atom Count: 9,751 
  • Modeled Residue Count: 1,159 
  • Deposited Residue Count: 1,168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein-ubiquinone oxidoreductase
A, B
584Sus scrofaMutation(s): 0 
EC: 1.5.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P55931 (Sus scrofa)
Explore P55931 
Go to UniProtKB:  P55931
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55931
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
G [auth A],
T [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
UQ5

Query on UQ5



Download:Ideal Coordinates CCD File
H [auth A],
U [auth B]
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
C34 H50 O4
NYFAQDMDAFCWPU-UVCHAVPFSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
F [auth A],
S [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
BHG

Query on BHG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
R [auth B]
hexyl beta-D-galactopyranoside
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.254 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.322α = 90
b = 154.322β = 90
c = 128.536γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Structure summary