1PP9

Bovine cytochrome bc1 complex with stigmatellin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern.

Huang, L.S.Cobessi, D.Tung, E.Y.Berry, E.A.

(2005) J Mol Biol 351: 573-597

  • DOI: 10.1016/j.jmb.2005.05.053
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formyl ...

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alphaA helix.


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex core protein I, mitochondrialA, N446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
Find proteins for P31800 (Bos taurus)
Explore P31800 
Go to UniProtKB:  P31800
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrialD, Q241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P00125 (Bos taurus)
Explore P00125 
Go to UniProtKB:  P00125
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrialE, R196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 14 kDa proteinF, S110Bos taurusMutation(s): 0 
Gene Names: UQCRB
EC: 1.10.2.2
Find proteins for P00129 (Bos taurus)
Explore P00129 
Go to UniProtKB:  P00129
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-CG, T81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
EC: 1.10.2.2
Find proteins for P13271 (Bos taurus)
Explore P13271 
Go to UniProtKB:  P13271
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 7.2 kDa proteinJ, W62Bos taurusMutation(s): 0 
Gene Names: UQCR10
EC: 1.10.2.2
Find proteins for P00130 (Bos taurus)
Explore P00130 
Go to UniProtKB:  P00130
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrialB, O439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
EC: 1.10.2.2
Find proteins for P23004 (Bos taurus)
Explore P23004 
Go to UniProtKB:  P23004
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome bC, P379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
EC: 1.10.2.2
Find proteins for P00157 (Bos taurus)
Explore P00157 
Go to UniProtKB:  P00157
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 11 kDa proteinH, U78Bos taurusMutation(s): 0 
Gene Names: UQCRH
EC: 1.10.2.2
Find proteins for P00126 (Bos taurus)
Explore P00126 
Go to UniProtKB:  P00126
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrialI, V78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download CCD File 
G, Q, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ
Query on UQ

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

Download CCD File 
A, C, D, G, N, P, Q, T
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
HEC
Query on HEC

Download CCD File 
D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA
Query on SMA

Download CCD File 
C, P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
JZR
Query on JZR

Download CCD File 
A, C, F, P, S
hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
B, O
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, C, O, P
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download CCD File 
A, C, D, P
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.117α = 90
b = 171.055β = 90
c = 227.204γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEmodel building
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 2.0: 2017-12-20
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations