5KLV

Structure of bos taurus cytochrome bc1 with fenamidone inhibited


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III.

Esser, L.Zhou, F.Zhou, Y.Xiao, Y.Tang, W.K.Yu, C.A.Qin, Z.Xia, D.

(2016) J Biol Chem 291: 25019-25031

  • DOI: https://doi.org/10.1074/jbc.M116.744391
  • Primary Citation of Related Structures:  
    5KKZ, 5KLI, 5KLV

  • PubMed Abstract: 

    Complex III or the cytochrome (cyt) bc 1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc 1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (Q P ) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the Q P site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc 1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc 1 of different species reveals a toxophore that appears to interact optimally with residues in the Q P site. The effect of modifications or additions to the toxophore on the binding to cyt bc 1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc 1 .


  • Organizational Affiliation

    the College of Science, China Agricultural University, Beijing 100193, China, and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial446Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31800 (Bos taurus)
Explore P31800 
Go to UniProtKB:  P31800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31800
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial439Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
Explore P23004 
Go to UniProtKB:  P23004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00157 (Bos taurus)
Explore P00157 
Go to UniProtKB:  P00157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00157
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial241Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00125 (Bos taurus)
Explore P00125 
Go to UniProtKB:  P00125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00125
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial196Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13272
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7110Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00129 (Bos taurus)
Explore P00129 
Go to UniProtKB:  P00129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00129
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 880Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13271 (Bos taurus)
Explore P13271 
Go to UniProtKB:  P13271
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13271
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrial78Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00126 (Bos taurus)
Explore P00126 
Go to UniProtKB:  P00126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial78Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13272
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 963Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00130 (Bos taurus)
Explore P00130 
Go to UniProtKB:  P00130
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00130
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1055Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07552 (Bos taurus)
Explore P07552 
Go to UniProtKB:  P07552
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07552
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
M [auth A],
X [auth D],
Z [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEF
Query on PEF

Download Ideal Coordinates CCD File 
W [auth D]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
8PE
Query on 8PE

Download Ideal Coordinates CCD File 
T [auth C](2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
PX4
Query on PX4

Download Ideal Coordinates CCD File 
AA [auth J]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
HEC
Query on HEC

Download Ideal Coordinates CCD File 
V [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
6PE
Query on 6PE

Download Ideal Coordinates CCD File 
BA [auth K],
L [auth A]
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
FNM
Query on FNM

Download Ideal Coordinates CCD File 
S [auth C](5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one
C17 H17 N3 O S
LMVPQMGRYSRMIW-KRWDZBQOSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
Y [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
U [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.986α = 90
b = 153.986β = 90
c = 592.713γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description