spacer
spacer

PDBsum entry 1l0n

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1l0n
Jmol
Contents
Protein chains
446 a.a. *
423 a.a. *
377 a.a. *
241 a.a. *
196 a.a. *
105 a.a. *
75 a.a. *
70 a.a. *
57 a.a. *
58 a.a. *
49 a.a. *
Ligands
HEM ×3
FES
* Residue conservation analysis
PDB id:
1l0n
Name: Oxidoreductase
Title: Native structure of bovine mitochondrial cytochrome bc1 comp
Structure: Ubiquinol-cytochromE C reductase complex core pro chain: a. Ubiquinol-cytochromE C reductase complex core pro chain: b. Synonym: complex iii subunit ii. Cytochrome b. Chain: c. Cytochrome c1, heme protein. Chain: d.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913
Biol. unit: Undecamer (from PQS)
Resolution:
2.60Å     R-factor:   0.261     R-free:   0.297
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31800  (QCR1_BOVIN) -  Cytochrome b-c1 complex subunit 1, mitochondrial
Seq:
Struc:
480 a.a.
446 a.a.
Protein chain
Pfam   ArchSchema ?
P23004  (QCR2_BOVIN) -  Cytochrome b-c1 complex subunit 2, mitochondrial
Seq:
Struc:
453 a.a.
423 a.a.
Protein chain
Pfam   ArchSchema ?
P00157  (CYB_BOVIN) -  Cytochrome b
Seq:
Struc:
379 a.a.
377 a.a.
Protein chain
Pfam   ArchSchema ?
P00125  (CY1_BOVIN) -  Cytochrome c1, heme protein, mitochondrial
Seq:
Struc:
325 a.a.
241 a.a.
Protein chain
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
196 a.a.
Protein chain
Pfam   ArchSchema ?
P00129  (QCR7_BOVIN) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
111 a.a.
105 a.a.*
Protein chain
Pfam   ArchSchema ?
P13271  (QCR8_BOVIN) -  Cytochrome b-c1 complex subunit 8
Seq:
Struc:
82 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
P00126  (QCR6_BOVIN) -  Cytochrome b-c1 complex subunit 6, mitochondrial
Seq:
Struc:
91 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
P00130  (QCR9_BOVIN) -  Cytochrome b-c1 complex subunit 9
Seq:
Struc:
64 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P07552  (QCR10_BOVIN) -  Cytochrome b-c1 complex subunit 10
Seq:
Struc:
56 a.a.
49 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains E, I: E.C.1.10.2.2  - Quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Quinol
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     oxidation-reduction process   13 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
    Added 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
21112412 A.Gómez-Durán, D.Pacheu-Grau, M.J.López-Pérez, J.Montoya, and E.Ruiz-Pesini (2011).
Mitochondrial pharma-Q-genomics: targeting the OXPHOS cytochrome b.
  Drug Discov Today, 16, 176-180.  
19928849 P.L.Zhao, L.Wang, X.L.Zhu, X.Huang, C.G.Zhan, J.W.Wu, and G.F.Yang (2010).
Subnanomolar inhibitor of cytochrome bc1 complex designed by optimizing interaction with conformationally flexible residues.
  J Am Chem Soc, 132, 185-194.  
19348884 F.Millett, and B.Durham (2009).
Chapter 5 Use of ruthenium photooxidation techniques to study electron transfer in the cytochrome bc1 complex.
  Methods Enzymol, 456, 95.  
19175316 R.E.Berry, M.N.Shokhirev, A.Y.Ho, F.Yang, T.K.Shokhireva, H.Zhang, A.Weichsel, W.R.Montfort, and F.A.Walker (2009).
Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes.
  J Am Chem Soc, 131, 2313-2327.
PDB code: 3fll
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.  
18996700 P.J.Crowley, E.A.Berry, T.Cromartie, F.Daldal, C.R.Godfrey, D.W.Lee, J.E.Phillips, A.Taylor, and R.Viner (2008).
The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.
  Bioorg Med Chem, 16, 10345-10355.
PDB code: 3cwb
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.  
17253777 S.Rajagukguk, S.Yang, C.A.Yu, L.Yu, B.Durham, and F.Millett (2007).
Effect of mutations in the cytochrome b ef loop on the electron-transfer reactions of the Rieske iron-sulfur protein in the cytochrome bc1 complex.
  Biochemistry, 46, 1791-1798.  
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.
PDB code: 2d2c
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.  
16433558 T.Teschner, L.Yatsunyk, V.Schünemann, H.Paulsen, H.Winkler, C.Hu, W.R.Scheidt, F.A.Walker, and A.X.Trautwein (2006).
Models of the membrane-bound cytochromes: mössbauer spectra of crystalline low-spin ferriheme complexes having axial ligand plane dihedral angles ranging from 0 degree to 90 degrees.
  J Am Chem Soc, 128, 1379-1389.  
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.  
16024040 L.S.Huang, D.Cobessi, E.Y.Tung, and E.A.Berry (2005).
Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.
  J Mol Biol, 351, 573-597.
PDB codes: 1pp9 1ppj 2a06
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.  
15313237 J.L.Smith, H.Zhang, J.Yan, G.Kurisu, and W.A.Cramer (2004).
Cytochrome bc complexes: a common core of structure and function surrounded by diversity in the outlying provinces.
  Curr Opin Struct Biol, 14, 432-439.  
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 code is shown on the right.