5OL2

The electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile.

Demmer, J.K.Pal Chowdhury, N.Selmer, T.Ermler, U.Buckel, W.

(2017) Nat Commun 8: 1577-1577

  • DOI: https://doi.org/10.1038/s41467-017-01746-3
  • Primary Citation of Related Structures:  
    5OL2

  • PubMed Abstract: 

    The electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the Clostridium difficile (EtfAB/Bcd) 4 complex in the dehydrogenase-conducting D-state, α-FAD (bound to domain II of EtfA) and δ-FAD (bound to Bcd) being 8 Å apart. Superimposing Acidaminococcus fermentans EtfAB onto C. difficile EtfAB/Bcd reveals a rotation of domain II of nearly 80°. Further rotation by 10° brings EtfAB into the bifurcating B-state, α-FAD and β-FAD (bound to EtfB) being 14 Å apart. This dual binding mode of domain II, substantiated by mutational studies, resembles findings in non-bifurcating EtfAB/acyl-CoA dehydrogenase complexes. In our proposed mechanism, NADH reduces β-FAD, which bifurcates. One electron goes to ferredoxin and one to α-FAD, which swings over to reduce δ-FAD to the semiquinone. Repetition affords a second reduced ferredoxin and δ-FADH - , which reduces crotonyl-CoA.


  • Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein large subunit
A, D
331Clostridioides difficileMutation(s): 0 
Gene Names: etfAetfA_4BN1095_140023BN1096_550022BN1097_530021SAMEA3374989_03962SAMEA3375004_04103SAMEA3375059_03747
UniProt
Find proteins for A0A125V455 (Peptoclostridium phage phiCDIF1296T)
Explore A0A125V455 
Go to UniProtKB:  A0A125V455
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125V455
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Electron transfer flavoprotein small subunit
B, E
260Clostridioides difficileMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A125V3V6 (Peptoclostridium phage phiCDIF1296T)
Explore A0A125V3V6 
Go to UniProtKB:  A0A125V3V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125V3V6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenase
C, F
378Clostridioides difficileMutation(s): 0 
Gene Names: acdAbcdBN1095_140021BN1096_550020BN1097_530019IM33_05890SAMEA3374973_01502SAMEA3374989_03964SAMEA3375004_04105SAMEA3375059_03749
EC: 1.3.8.1 (PDB Primary Data), 1.3.99 (PDB Primary Data)
UniProt
Find proteins for A0A125V4E7 (Peptoclostridium phage phiCDIF1296T)
Explore A0A125V4E7 
Go to UniProtKB:  A0A125V4E7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125V4E7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COS
Query on COS

Download Ideal Coordinates CCD File 
K [auth C],
R [auth F]
COENZYME A PERSULFIDE
C21 H36 N7 O16 P3 S2
REVPHPVBPSIEKM-IBOSZNHHSA-N
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
J [auth C],
M [auth D],
O [auth E],
Q [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
L [auth C],
N [auth D],
P [auth E],
S [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.06α = 90
b = 177.06β = 90
c = 493.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research FoundationGermany--
SYNMIKROGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description