7KOE | pdb_00007koe

Electron bifurcating flavoprotein Fix/EtfABCX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KOE

This is version 1.1 of the entry. See complete history

Literature

Cryoelectron microscopy structure and mechanism of the membrane-associated electron-bifurcating flavoprotein Fix/EtfABCX.

Feng, X.Schut, G.J.Lipscomb, G.L.Li, H.Adams, M.W.W.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2016978118
  • Primary Citation Related Structures: 
    7KOE

  • PubMed Abstract: 

    The electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX), also known as FixABCX for its role in nitrogen-fixing organisms, is a member of a family of electron-transferring flavoproteins that catalyze electron bifurcation. EtfABCX enables endergonic reduction of ferredoxin ( E °' ∼-450 mV) using NADH ( E °' -320 mV) as the electron donor by coupling this reaction to the exergonic reduction of menaquinone ( E °' -80 mV). Here we report the 2.9 Å structure of EtfABCX, a membrane-associated flavin-based electron bifurcation (FBEB) complex, from a thermophilic bacterium. EtfABCX forms a superdimer with two membrane-associated EtfCs at the dimer interface that contain two bound menaquinones. The structure reveals that, in contrast to previous predictions, the low-potential electrons bifurcated from EtfAB are most likely directly transferred to ferredoxin, while high-potential electrons reduce the quinone via two [4Fe-4S] clusters in EtfX. Surprisingly, EtfX shares remarkable structural similarity with mammalian [4Fe-4S] cluster-containing ETF ubiquinone oxidoreductase (ETF-QO), suggesting an unexpected evolutionary link between bifurcating and nonbifurcating systems. Based on this structure and spectroscopic studies of a closely related EtfABCX, we propose a detailed mechanism of the catalytic cycle and the accompanying structural changes in this membrane-associated FBEB system.


  • Organizational Affiliation
    • Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503.

Macromolecule Content 

  • Total Structure Weight: 266.57 kDa 
  • Atom Count: 18,348 
  • Modeled Residue Count: 2,296 
  • Deposited Residue Count: 2,328 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein, beta subunit
A, E
296Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_1530
UniProt
Find proteins for Q9X1L6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1L6 
Go to UniProtKB:  Q9X1L6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1L6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein, alpha subunit
B, F
338Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: Tmari_1539
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein-quinone oxidoreductase FixC
C, G
438Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: Tmari_1540
EC: 1.5.5
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-like protein
D, H
92Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: Tmari_1541

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
I [auth A]
J [auth B]
K [auth C]
O [auth E]
P [auth F]
I [auth A],
J [auth B],
K [auth C],
O [auth E],
P [auth F],
Q [auth G]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MQ7
(Subject of Investigation/LOI)

Query on MQ7



Download:Ideal Coordinates CCD File
L [auth C],
R [auth G]
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
M [auth D],
N [auth D],
S [auth H],
T [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0020085
Department of Energy (DOE, United States)United StatesDE-FG02-95ER20175

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references