Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 22-mer - A2B2C2D2E2F2G2H2I2J2K2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 22-mer - A4B2C2D2E2F2G2H2I2J2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 250.15 kDa 
• Atom Count: 16866 
• Modelled Residue Count: 2080 
• Deposited Residue Count: 2165 
• Unique protein chains: 11

6NHG

Rhodobacter sphaeroides Mitochondrial respiratory chain complex

• DOI: 10.2210/pdb6NHG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Expression System: Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-12-21 Released: 2019-06-19 
• Deposition Author(s): Xia, D., Zhou, F., Esser, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 

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

• PubMed: 31182483 
• DOI: 10.1074/jbc.RA119.008381
• Primary Citation of Related Structures:  
  6NHH, 6NHG, 6NIN


• PubMed Abstract: 
  

Cytochrome bc ₁ complexes (cyt bc ₁ ), also known as complex III in mitochondria, are components of the cellular respiratory chain and of the photosynthetic apparatus of non-oxygenic 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 bc ₁ from the photosynthetic bacterium Rhodobacter sphaeroides in complex with the fungicide azoxystrobin. Unlike cyt bc ₁ inhibitors stigmatellin and famoxadone that immobilize the ISP, azoxystrobin causes the ISP-ED 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 Q-cycle mechanism of cyt bc ₁ function.

---

Organizational Affiliation: 

Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A	446	Bos taurus	Mutation(s): 0  Gene Names: UQCRC1 Membrane Entity: Yes
UniProt
Find proteins for P31800 (Bos taurus) Explore P31800  Go to UniProtKB:  P31800

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B	439	Bos taurus	Mutation(s): 0  Gene Names: UQCRC2 Membrane Entity: Yes
UniProt
Find proteins for P23004 (Bos taurus) Explore P23004  Go to UniProtKB:  P23004

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C	379	Bos taurus	Mutation(s): 0  Gene Names: MT-CYB, COB, CYTB, MTCYB Membrane Entity: Yes
UniProt
Find proteins for P00157 (Bos taurus) Explore P00157  Go to UniProtKB:  P00157

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D	241	Bos taurus	Mutation(s): 0  Gene Names: CYC1 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00125 (Bos taurus) Explore P00125  Go to UniProtKB:  P00125

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E	196	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272  Go to UniProtKB:  P13272

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F	110	Bos taurus	Mutation(s): 0  Gene Names: UQCRB Membrane Entity: Yes
UniProt
Find proteins for P00129 (Bos taurus) Explore P00129  Go to UniProtKB:  P00129

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G	80	Bos taurus	Mutation(s): 0  Gene Names: UQCRQ Membrane Entity: Yes
UniProt
Find proteins for P13271 (Bos taurus) Explore P13271  Go to UniProtKB:  P13271

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H	78	Bos taurus	Mutation(s): 0  Gene Names: UQCRH Membrane Entity: Yes
UniProt
Find proteins for P00126 (Bos taurus) Explore P00126  Go to UniProtKB:  P00126

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I	78	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272  Go to UniProtKB:  P13272

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J	63	Bos taurus	Mutation(s): 0  Gene Names: UQCR10 Membrane Entity: Yes
UniProt
Find proteins for P00130 (Bos taurus) Explore P00130  Go to UniProtKB:  P00130

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	K	55	Bos taurus	Mutation(s): 0  Gene Names: UQCR11, UQCR Membrane Entity: Yes
UniProt
Find proteins for P07552 (Bos taurus) Explore P07552  Go to UniProtKB:  P07552

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL (Subject of Investigation/LOI)	M [auth A], S [auth D], U [auth G]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
8PE (Subject of Investigation/LOI)	Q [auth C]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C37 H74 N O8 P RFJQNULIDFTTLL-PGUFJCEWSA-N
MC3 (Subject of Investigation/LOI)	V [auth J]	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE C36 H72 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-N
HEC (Subject of Investigation/LOI)	R [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)	N [auth C], O [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
6PE (Subject of Investigation/LOI)	L [auth A], W [auth K]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C17 H33 N O8 P PELYUHWUVHDSSU-OAHLLOKOSA-M
AZO (Subject of Investigation/LOI)	P [auth C]	METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE C22 H17 N3 O5 WFDXOXNFNRHQEC-GHRIWEEISA-N
FES	T [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AZO	BindingDB:  6NHG	Ki: 298 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.181	α = 90
b = 154.181	β = 90
c = 598.18	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2018-12-21 
• Released Date: 2019-06-19 
Deposition Author(s): Xia, D., Zhou, F., Esser, L.

Revision History  

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