spacer
spacer
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB-id
1l0l
Asymmetric unit
Main view
    Jmol     Help!  
Contents
Description
Header details
Header records
References
PROCHECK
Protein chains
446 a.a. *
423 a.a. *
377 a.a. *
240 a.a. *
196 a.a. *
109 a.a. *
79 a.a. *
78 a.a. *
57 a.a. *
60 a.a. *
53 a.a. *
Ligands
HEM ×3
FMX
FES

* Residue conservation analysis
Tools
Image Generation
AstexViewer™@PDBe
Run PROCHECK
Clefts Calculation
  
  Biological unit*, 22mer
(*as deduced by PQS)
PDB id: 1l0l
Name: Oxidoreductase
Title: Structure of bovine mitochondrial cytochrome bc1 complex with a bound fungicide famoxadone

Structure:
Ubiquinol-cytochromE C reductase complex core protein i. Chain: a. Ubiquinol-cytochromE C reductase complex core protein 2. Chain: b. Synonym: complex iii subunit ii. Cytochrome b. Chain: c.

Source:
Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913

Biological unit:
22mer (from PQS)

UniProt:
Chain A: P31800 (QCR1_BOVIN)
Pfam  
Seq:
Struc:
Seq: 480 a.a.
Struc: 446 a.a.

Chain B: P23004 (QCR2_BOVIN)
Pfam  
Seq:
Struc:
Seq: 453 a.a.
Struc: 423 a.a.

Chain C: P00157 (CYB_BOVIN)
Pfam  
Seq:
Struc:
Seq: 379 a.a.
Struc: 377 a.a.

Chain D: P00125 (CY1_BOVIN)
Pfam  
Seq:
Struc:
Seq: 325 a.a.
Struc: 240 a.a.

Chain E: P13272 (UCRI_BOVIN)
Pfam  
Seq:
Struc:
Seq: 274 a.a.
Struc: 196 a.a.

Chain F: P00129 (QCR7_BOVIN)
Pfam  
Seq: 111 a.a.
Struc: 109 a.a.*

Chain G: P13271 (QCR8_BOVIN)
Pfam  
Seq: 82 a.a.
Struc: 79 a.a.

Chain H: P00126 (QCR6_BOVIN)
Pfam  
Seq: 91 a.a.
Struc: 78 a.a.

Chain I: P13272 (UCRI_BOVIN)
Pfam  
Seq:
Struc:
Seq: 274 a.a.
Struc: 57 a.a.

Chain J: P00130 (QCR9_BOVIN)
Pfam  
Seq: 64 a.a.
Struc: 60 a.a.

Chain K: P07552 (QCR10_BOVIN)
Pfam  
Seq: 56 a.a.
Struc: 53 a.a.*
Key:    PfamA domain
 Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme class:
Chains E, I: E.C.1.10.2.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:
QH2 + 2 ferricytochrome c = Q + 2 ferrocytochrome c + 2 H+ (see diagram below)

Resolution:
2.35Å

R-factor:
0.260

R-free:
0.306

Authors:
X.Gao,X.Wen,C.A.Yu,L.Esser,S.Tsao,B.Quinn,L.Zhang,L.Yu,D.Xia

Key ref:
X.Gao et al. (2002). The crystal structure of mitochondrial cytochrome bc1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition.. Biochemistry, 41, 11692-11702. [PubMed id: 12269811] [DOI: 10.1021/bi026252p]

Date:
11-Feb-02

Release date:
08-Apr-03
Quick_links
RCSB
PDBe
SRS
MMDB
JenaLib
OCA
Proteopedia
CATH
SCOP
FSSP
HSSP
PDBSWS
OPM
PQS
CSA
PROCOGNATE
ProSAT
Whatcheck
Procheck
Go to PROCHECK summary
spacer
spacer
Enzyme reaction for E.C.1.10.2.2


QH(2)
+
2 × ferricytochrome c
=
Q
+

2 × ferrocytochrome c
Bound ligand (Het Group name = HEM)
matches with 70.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

 
    Key reference    
 
 
DOI no: 10.1021/bi026252p Biochemistry 41:11692-11702 (2002)
PubMed id: 12269811  
 
 
The crystal structure of mitochondrial cytochrome bc1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition.
X.Gao, X.Wen, C.Yu, L.Esser, S.Tsao, B.Quinn, L.Zhang, L.Yu, D.Xia.
 
  ABSTRACT  
 
Ubiquinol cytochrome c oxido-reductase (EC. 1.10.2.2, bc1) is an integral membrane protein complex essential to cellular respiration. Structures of the 11-subunit mitochondrial bc1 complex were determined with and without the fungicide famoxadone. Specific inhibition by famoxadone is achieved through a coordinated optimization of aromatic-aromatic interactions where conformational rearrangements in famoxadone and in residues lining the inhibitor-binding pocket produce a network of aromatic-aromatic interactions that mimic the crystal lattice of benzene. The profound aromatic-aromatic interactions as supported by prior mutagenesis provide a structural basis for specific protein-ligand interaction in a hydrophobic environment. Dramatic conformational changes, both in cyt. b and ISP subunits in the inhibitor-protein complex, confer experimental evidence for a functional role of cytochrome b in the induced conformational arrest of ISP and allow the identification of a possible intrasubunit signal transduction pathway that controls the movement of ISP. These results support an inhibitory mechanism that is consistent with the requirement for ISP movement in the electron transfer of this complex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18418633 E.A.Berry, and F.A.Walker (2008).
Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins.
  J Biol Inorg Chem, 13, 481-498.  
18039651 L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, and D.Xia (2008).
Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.
  J Biol Chem, 283, 2846-2857.
PDB codes: 2qjk 2qjp 2qjy
18093133 N.Fisher, and B.Meunier (2008).
Molecular basis of resistance to cytochrome bc1 inhibitors.
  FEMS Yeast Res, 8, 183-192.  
17457691 D.Xia, L.Esser, L.Yu, and C.A.Yu (2007).
Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc1 complex.
  Photosynth Res, 92, 17-34.  
16586113 F.A.Walker (2006).
The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography.
  J Biol Inorg Chem, 11, 391-397.  
16371475 J.Yan, G.Kurisu, and W.A.Cramer (2006).
Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex.
  Proc Natl Acad Sci U S A, 103, 69-74.  
16924113 L.Esser, X.Gong, S.Yang, L.Yu, C.A.Yu, and D.Xia (2006).
Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex.
  Proc Natl Acad Sci U S A, 103, 13045-13050.
PDB codes: 2fyn 2fyu
16641489 T.Páli, D.Bashtovyy, and D.Marsh (2006).
Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures.
  Protein Sci, 15, 1153-1161.  
15718226 J.J.Kessl, K.H.Ha, A.K.Merritt, B.B.Lange, P.Hill, B.Meunier, S.R.Meshnick, and B.L.Trumpower (2005).
Cytochrome b mutations that modify the ubiquinol-binding pocket of the cytochrome bc1 complex and confer anti-malarial drug resistance in Saccharomyces cerevisiae.
  J Biol Chem, 280, 17142-17148.  
15615714 X.Gong, L.Yu, D.Xia, and C.A.Yu (2005).
Evidence for electron equilibrium between the two hemes bL in the dimeric cytochrome bc1 complex.
  J Biol Chem, 280, 9251-9257.  
14977419 A.R.Crofts (2004).
The cytochrome bc1 complex: function in the context of structure.
  Annu Rev Physiol, 66, 689-733.  
14716012 E.Ruiz-Pesini, D.Mishmar, M.Brandon, V.Procaccio, and D.C.Wallace (2004).
Effects of purifying and adaptive selection on regional variation in human mtDNA.
  Science, 303, 223-226.  
14526088 G.Kurisu, H.Zhang, J.L.Smith, and W.A.Cramer (2003).
Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
  Science, 302, 1009-1014.
PDB codes: 1um3 1vf5
12525495 K.Xiao, G.Engstrom, S.Rajagukguk, C.A.Yu, L.Yu, B.Durham, and F.Millett (2003).
Effect of famoxadone on photoinduced electron transfer between the iron-sulfur center and cytochrome c1 in the cytochrome bc1 complex.
  J Biol Chem, 278, 11419-11426.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.