3H1L

Chicken cytochrome BC1 complex with ascochlorin bound at QO and QI sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ascochlorin is a novel, specific inhibitor of the mitochondrial cytochrome bc(1) complex.

Berry, E.A.Huang, L.S.Lee, D.W.Daldal, F.Nagai, K.Minagawa, N.

(2010) Biochim.Biophys.Acta 1797: 360-370

  • DOI: 10.1016/j.bbabio.2009.12.003

  • PubMed Abstract: 
  • Ascochlorin is an isoprenoid antibiotic that is produced by the phytopathogenic fungus Ascochyta viciae. Similar to ascofuranone, which specifically inhibits trypanosome alternative oxidase by acting at the ubiquinol binding domain, ascochlorin is al ...

    Ascochlorin is an isoprenoid antibiotic that is produced by the phytopathogenic fungus Ascochyta viciae. Similar to ascofuranone, which specifically inhibits trypanosome alternative oxidase by acting at the ubiquinol binding domain, ascochlorin is also structurally related to ubiquinol. When added to the mitochondrial preparations isolated from rat liver, or the yeast Pichia (Hansenula) anomala, ascochlorin inhibited the electron transport via CoQ in a fashion comparable to antimycin A and stigmatellin, indicating that this antibiotic acted on the cytochrome bc(1) complex. In contrast to ascochlorin, ascofuranone had much less inhibition on the same activities. On the one hand, like the Q(i) site inhibitors antimycin A and funiculosin, ascochlorin induced in H. anomala the expression of nuclear-encoded alternative oxidase gene much more strongly than the Q(o) site inhibitors tested. On the other hand, it suppressed the reduction of cytochrome b and the generation of superoxide anion in the presence of antimycin A(3) in a fashion similar to the Q(o) site inhibitor myxothiazol. These results suggested that ascochlorin might act at both the Q(i) and the Q(o) sites of the fungal cytochrome bc(1) complex. Indeed, the altered electron paramagnetic resonance (EPR) lineshape of the Rieske iron-sulfur protein, and the light-induced, time-resolved cytochrome b and c reduction kinetics of Rhodobacter capsulatus cytochrome bc(1) complex in the presence of ascochlorin demonstrated that this inhibitor can bind to both the Q(o) and Q(i) sites of the bacterial enzyme. Additional experiments using purified bovine cytochrome bc(1) complex showed that ascochlorin inhibits reduction of cytochrome b by ubiquinone through both Q(i) and Q(o) sites. Moreover, crystal structure of chicken cytochrome bc(1) complex treated with excess ascochlorin revealed clear electron densities that could be attributed to ascochlorin bound at both the Q(i) and Q(o) sites. Overall findings clearly show that ascochlorin is an unusual cytochrome bc(1) inhibitor that acts at both of the active sites of this enzyme.


    Organizational Affiliation

    SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
A, N
446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX31 (Gallus gallus)
Go to UniProtKB:  D0VX31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
B, O
441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX29 (Gallus gallus)
Go to UniProtKB:  D0VX29
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P18946 (Gallus gallus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P18946
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
D, Q
241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX26 (Gallus gallus)
Go to UniProtKB:  D0VX26
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, R
196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
F, S
110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
Go to UniProtKB:  D0VX30
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
G, T
81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX32 (Gallus gallus)
Go to UniProtKB:  D0VX32
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
H, U
77Gallus gallusMutation(s): 0 
Gene Names: UQCRH
Find proteins for D0VX28 (Gallus gallus)
Go to Gene View: UQCRH
Go to UniProtKB:  D0VX28
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
I, V
47Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
J, W
61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX27 (Gallus gallus)
Go to UniProtKB:  D0VX27
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3H1
Query on 3H1

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C, P
3-chloro-4,6-dihydroxy-2-methyl-5-{(2E,4E)-3-methyl-5-[(1R,2R,6R)-1,2,6-trimethyl-3-oxocyclohexyl]penta-2,4-dien-1-yl}benzaldehyde
ASCOCHLORIN
C23 H29 Cl O4
SETVRSKZJJWOPA-FLDGXQSCSA-N
 Ligand Interaction
CDL
Query on CDL

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Download CCD File 
C, G, P, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GOL
Query on GOL

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C, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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C, P
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

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D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
BOG
Query on BOG

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D, R
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
PEE
Query on PEE

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A, C, E, P, R
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
I, V
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 174.139α = 90.00
b = 182.364β = 90.00
c = 241.626γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
Blu-Icedata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description