6ZFU

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor RKA066

• PDB DOI: https://doi.org/10.2210/pdb6ZFU/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2020-06-17 Released: 2021-06-30 
• Deposition Author(s): Amporndanai, K., O'Neill, P.M., Hong, W.D., Amewu, R.K., Pidathala, C., Berry, N.G., Biagini, G.A., Leung, S.C., Hasnain, S.S., Antonyuk, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials

Amporndanai, K., O'Neill, P.M., Hong, W.D., Amewu, R.K., Pidathala, C., Berry, N., Biangini, G.A., Leung, S.C., Hasnain, S.S., Antonyuk, S.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A1B1C1D1E1F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B1C1D1E1F1G1H1I1 

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

Biological Assembly Evidence: scanning transmission electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 237.96 kDa 
• Atom Count: 16,290 
• Modelled Residue Count: 2,015 
• Deposited Residue Count: 2,020 
• Unique protein chains: 10

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	A	444	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P31800 (Bos taurus) Go to UniProtKB:  P31800

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	B	420	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P23004 (Bos taurus) Go to UniProtKB:  P23004

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C	378	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00157 (Bos taurus) Go to UniProtKB:  P00157

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D	239	Bos taurus	Mutation(s): 0  EC: 7.1.1.8
UniProt
Find proteins for P00125 (Bos taurus) 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  EC: 7.1.1.8
UniProt
Find proteins for P13272 (Bos taurus) Go to UniProtKB:  P13272

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F	99	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00129 (Bos taurus) Go to UniProtKB:  P00129

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	G	74	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P13271 (Bos taurus) Go to UniProtKB:  P13271

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	H	65	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00126 (Bos taurus) Go to UniProtKB:  P00126

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	I	46	Bos taurus	Mutation(s): 0  EC: 7.1.1.8
UniProt
Find proteins for P13272 (Bos taurus) Go to UniProtKB:  P13272

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	J	59	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00130 (Bos taurus) Go to UniProtKB:  P00130

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	BA [auth E], M [auth A], S [auth C], X [auth D]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE	AA [auth E], T [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N
PX4	Z [auth E]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C36 H73 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-O
HEC	V [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM	N [auth C], O [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
LMT	P [auth C]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
JHE (Subject of Investigation/LOI)	U [auth C]	3-methyl-1-oxidanyl-2-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]quinolin-4-one C24 H18 F3 N O3 ZSBSILZBHTWRSX-UHFFFAOYSA-N
6PE	L [auth A]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C17 H33 N O8 P PELYUHWUVHDSSU-OAHLLOKOSA-M
PG4	K [auth A], Q [auth C], R [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES	Y [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4	CA [auth F], DA [auth G], EA [auth G], FA [auth G], W [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.74	α = 90
b = 210.74	β = 90
c = 343.935	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Amporndanai, K., O'Neill, P.M., Hong, W.D., Amewu, R.K., Pidathala, C., Berry, N.G., Biagini, G.A., Leung, S.C., Hasnain, S.S., Antonyuk, S.V.

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 2.0: 2024-01-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary