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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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

    From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, xiad@mail.nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane Entity: Yes 
UniProt
Find proteins for P31800 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
UniProt
Find proteins for P00157 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F110Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G80Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH78Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J63Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10K55Bos taurusMutation(s): 0 
Gene Names: UQCR11UQCR
Membrane Entity: Yes 
UniProt
Find proteins for P07552 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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M [auth A], X [auth D], Z [auth G]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PEF (Subject of Investigation/LOI)
Query on PEF

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W [auth D]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
8PE (Subject of Investigation/LOI)
Query on 8PE

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T [auth C](2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
 Ligand Interaction
PX4 (Subject of Investigation/LOI)
Query on PX4

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AA [auth J]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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V [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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Q [auth C], R [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
6PE (Subject of Investigation/LOI)
Query on 6PE

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BA [auth K], L [auth A]1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
 Ligand Interaction
FNM (Subject of Investigation/LOI)
Query on FNM

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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
 Ligand Interaction
FES
Query on FES

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Y [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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N [auth B], O [auth B], P [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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U [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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

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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