5OKD

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery.

Amporndanai, K.Johnson, R.M.O'Neill, P.M.Fishwick, C.W.G.Jamson, A.H.Rawson, S.Muench, S.P.Hasnain, S.S.Antonyuk, S.V.

(2018) IUCrJ 5: 200-210

  • DOI: 10.1107/S2052252518001616
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome <i>bc </i> <sub>1 </sub>, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochr ...

    Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc 1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.


    Organizational Affiliation

    Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England.,School of Chemistry, University of Leeds, Leeds LS2 9JT, England.,Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, England.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A
480Bos taurusMutation(s): 0 
Gene Names: UQCRC1
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
453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
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)
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
325Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
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
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
111Bos taurusMutation(s): 0 
Gene Names: UQCRB
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
82Bos taurusMutation(s): 0 
Gene Names: UQCRQ
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
91Bos taurusMutation(s): 0 
Gene Names: UQCRH
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
47Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
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
64Bos taurusMutation(s): 0 
Gene Names: UQCR10
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9XE
Query on 9XE

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C
7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one
C23 H17 F3 N2 O3
ZZCQNODHORIHJA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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D, E, F, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CDL
Query on CDL

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C, D, E
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PG4
Query on PG4

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A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

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D
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
LMT
Query on LMT

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C
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
6PE
Query on 6PE

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A
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
 Ligand Interaction
PX4
Query on PX4

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Download CCD File 
E
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
PEE
Query on PEE

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Download CCD File 
C, E
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 209.871α = 90.00
b = 209.871β = 90.00
c = 342.097γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references
  • Version 1.2: 2018-05-30
    Type: Data collection, Database references, Structure summary