3H1K

Chicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex

Berry, E.A.Zhang, Z.Bellamy, H.D.Huang, L.

(2000) Biochim.Biophys.Acta 1459: 440-448


  • PubMed Abstract: 
  • The chicken mitochondrial ubiquinol cytochrome c oxidoreductase (bc(1) complex) is inhibited by Zn(2+) ions, but with higher K(i) ( approximately 3 microM) than the corresponding bovine enzyme. When equilibrated with mother liquor containing 200 micr ...

    The chicken mitochondrial ubiquinol cytochrome c oxidoreductase (bc(1) complex) is inhibited by Zn(2+) ions, but with higher K(i) ( approximately 3 microM) than the corresponding bovine enzyme. When equilibrated with mother liquor containing 200 microM ZnCl(2) for 7 days, the crystalline chicken bc(1) complex specifically binds Zn(2+) at 4 sites representing two sites on each monomer in the dimer. These two sites are close to the stigmatellin-binding site, taken to be center Q(o) of the Q-cycle mechanism, and are candidates for the inhibitory site. One binding site is actually in the hydrophobic channel between the Q(o) site and the bulk lipid phase, and may interfere with quinone binding. The other is in a hydrophilic area between cytochromes b and c(1), and might interfere with the egress of protons from the Q(o) site to the intermembrane aqueous medium. No zinc was bound near the putative proteolytic active site of subunits 1 and 2 (homologous to mitochondrial processing peptidase) under these conditions.


    Organizational Affiliation

    lawrence Berkeley National Laboratory, University of California, USA. eaberry@lbl.gov




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 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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C, P
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CDL
Query on CDL

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C, D, P, Q
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
IKR
Query on IKR

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C, P
methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate
C19 H20 I N O4
QNSHGJNFUSNVMK-DYTRJAOYSA-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
UQ
Query on UQ

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C, P
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
BOG
Query on BOG

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D, P, Q
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

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZNKi: 3000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 171.717α = 90.00
b = 181.297β = 90.00
c = 241.288γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance