6NHG

Rhodobacter sphaeroides Mitochondrial respiratory chain complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit.

Esser, L., Zhou, F., Yu, C.A., Xia, D.

(2019) J.Biol.Chem. 294: 12007-12019

  • DOI: 10.1074/jbc.RA119.008381
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Cytochrome bc1 complexes (cyt bc1), also known as Complex III in mitochondria, are components of the cellular respiratory chain and of the photosynthetic apparatus of nonoxygeneic photosynthetic bacteria. They catalyze electron transfer (ET) from ubi ...

    Cytochrome bc1 complexes (cyt bc1), also known as Complex III in mitochondria, are components of the cellular respiratory chain and of the photosynthetic apparatus of nonoxygeneic photosynthetic bacteria. They catalyze electron transfer (ET) from ubiquinol to cytochrome c and concomitantly translocate protons across the membrane, contributing to the cross-membrane potential essential for a myriad of cellular activities. This ET-coupled proton translocation reaction requires a gating mechanism that ensures bifurcated electron flow. Here, we report the observation of the Rieske iron-sulfur protein (ISP) in a mobile state, as revealed by the crystal structure of cyt bc1 from the photosynthetic bacterium Rhodobacter sphaeroides in complex with the fungicide azoxystrobin. Unlike cyt bc1 inhibitors stigmatellin and famoxadone that immobilize the ISP, azoxystrobin causes the ISP to separate from the cyt b subunit and to remain in a mobile state. Analysis of anomalous scattering signals from the iron-sulfur cluster of the ISP suggests the existence of a trajectory for electron delivery. This work supports and solidifies the hypothesis that the bimodal conformation switch of the ISP provides a gating mechanism for bifurcated ET, which is essential to the Qcycle mechanism of cyt bc1 function.

    Organizational Affiliation: 

    National Institutes of Health, United States.,Oklahoma State University, United States.,Laboratory of Cell Biology, National Institutes of Health, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A
446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P31800 (Bos taurus)
Go to Gene View: UQCRC1
Go to UniProtKB:  P31800
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrial
B
439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P23004 (Bos taurus)
Go to Gene View: UQCRC2
Go to UniProtKB:  P23004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
379Bos taurusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00157 (Bos taurus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P00157
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial
D
241Bos taurusMutation(s): 0 
Gene Names: CYC1
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00125 (Bos taurus)
Go to Gene View: CYC1
Go to UniProtKB:  P00125
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E
196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
F
110Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00129 (Bos taurus)
Go to Gene View: UQCRB
Go to UniProtKB:  P00129
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8
G
80Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P13271 (Bos taurus)
Go to Gene View: UQCRQ
Go to UniProtKB:  P13271
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6, mitochondrial
H
78Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00126 (Bos taurus)
Go to Gene View: UQCRH
Go to UniProtKB:  P00126
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
I
78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9
J
63Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 10
K
55Bos taurusMutation(s): 0 
Gene Names: UQCR11 (UQCR)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P07552 (Bos taurus)
Go to Gene View: UQCR11
Go to UniProtKB:  P07552
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MC3
Query on MC3
Download SDF File 
Download CCD File 
J
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
 Ligand Interaction
CDL
Query on CDL
Download SDF File 
Download CCD File 
A, D, G
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
FES
Query on FES
Download SDF File 
Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC
Download SDF File 
Download CCD File 
D
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
8PE
Query on 8PE
Download SDF File 
Download CCD File 
C
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
 Ligand Interaction
6PE
Query on 6PE
Download SDF File 
Download CCD File 
A, K
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
 Ligand Interaction
AZO
Query on AZO
Download SDF File 
Download CCD File 
C
METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE
AZOXYSTROBIN
C22 H17 N3 O5
WFDXOXNFNRHQEC-GHRIWEEISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.251 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.181α = 90.00
b = 154.181β = 90.00
c = 598.180γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection, Database references