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Entry
Database: PDB / ID: 4pd4
TitleStructural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action
Components
  • (Cytochrome b-c1 complex subunit ...) x 7
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Ig kappa chain V-V region HP 124E1
  • Igh protein
KeywordsOXIDOREDUCTASE/INHIBITOR / Cytochrome bc1 complex / Membrane protein complex / antimalarial drug / inhibitor / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


Respiratory electron transport / mitochondrial crista / mitochondrial respiratory chain complex III assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / immunoglobulin complex / mitochondrial respirasome ...Respiratory electron transport / mitochondrial crista / mitochondrial respiratory chain complex III assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / immunoglobulin complex / mitochondrial respirasome / oxidative phosphorylation / ubiquinol-cytochrome-c reductase activity / integral component of mitochondrial inner membrane / electron transport chain / immunoglobulin production / mitochondrial ATP synthesis coupled proton transport / mitochondrial electron transport, ubiquinol to cytochrome c / aerobic respiration / nuclear periphery / 2 iron, 2 sulfur cluster binding / catalytic activity / mitochondrial intermembrane space / metalloendopeptidase activity / mitochondrial inner membrane / adaptive immune response / immune response / heme binding / mitochondrion / extracellular space / integral component of membrane / metal ion binding / cytosol
Immunoglobulin V-set domain / Cytochrome c-like domain / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex, subunit 6 / Immunoglobulin subtype / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b/b6, N-terminal / Cytochrome b/b6, C-terminal / Rieske iron-sulphur protein, C-terminal ...Immunoglobulin V-set domain / Cytochrome c-like domain / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex, subunit 6 / Immunoglobulin subtype / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b/b6, N-terminal / Cytochrome b/b6, C-terminal / Rieske iron-sulphur protein, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Immunoglobulin-like domain / Peptidase M16, C-terminal / Cytochrome b-c1 complex subunit 9 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Peptidase M16, N-terminal / Cytochrome b-c1 complex subunit 9 superfamily / Immunoglobulin-like fold / Rieske iron-sulphur protein / Di-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b/b6-like domain superfamily / Cytochrome b / Cytochrome b/b6, C-terminal domain superfamily / Immunoglobulin-like domain superfamily / Cytochrome c1 / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c-like domain superfamily / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c family profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6 N-terminal region profile. / Ig-like domain profile. / Insulinase family, zinc-binding region signature. / Immunoglobulin V-set domain / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Peptidase M16 inactive domain / UcrQ family / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge protein / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome C1 family / Insulinase (Peptidase family M16) / Rieske [2Fe-2S] domain / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome b-c1 complex subunit 7 superfamily
Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Ig kappa chain V-V region HP 124E1 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 6 / Uncharacterized protein
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 Å
AuthorsBirth, D. / Kao, W.-C. / Hunte, C.
Funding supportGermany , 2件
OrganizationGrant numberCountry
German Research FoundationCRC 746, CRC 992Germany
Excellence Initiative of the German Federal and State GovernmentsEXC 294 BIOSSGermany
CitationJournal: Nat Commun / Year: 2014
Title: Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action.
Authors: Birth, D. / Kao, W.C. / Hunte, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 17, 2014 / Release: Jun 11, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 11, 2014Structure modelrepositoryInitial release
1.1Jun 18, 2014Structure modelDatabase references
1.2Dec 24, 2014Structure modelDatabase references
1.3Apr 20, 2016Structure modelNon-polymer description
1.4Nov 22, 2017Structure modelAdvisory / Derived calculations / Refinement descriptionpdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software_pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
J: Igh protein
K: Ig kappa chain V-V region HP 124E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,15022
Polymers244,80511
Non-polymers6,34511
Water0
1
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
J: Igh protein
K: Ig kappa chain V-V region HP 124E1
hetero molecules

A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
J: Igh protein
K: Ig kappa chain V-V region HP 124E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,30044
Polymers489,61122
Non-polymers12,68922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area97160 Å2
ΔGint-744 kcal/mol
Surface area151430 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)212.260, 150.880, 143.090
Angle α, β, γ (deg.)90.000, 115.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Cytochrome b-c1 complex subunit ... , 7 types, 7 molecules ABEFGHI

#1: Protein/peptide Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 47445.242 Da / Num. of mol.: 1 / Fragment: UNP residues 27-457 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07256
#2: Protein/peptide Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 38751.918 Da / Num. of mol.: 1 / Fragment: UNP residues 17-368 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07257
#5: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 20122.955 Da / Num. of mol.: 1 / Fragment: UNP residues 31-215 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08067, quinol-cytochrome-c reductase
#6: Protein/peptide Cytochrome b-c1 complex subunit 6 / Complex III subunit 6 / Complex III subunit VI / Cytochrome c1 non-heme 17 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 17 kDa protein


Mass: 8854.792 Da / Num. of mol.: 1 / Fragment: UNP residues 74-147 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00127
#7: Protein/peptide Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c reductase c reductase complex 14 kDa protein


Mass: 14452.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00128
#8: Protein/peptide Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c reductase complex 11 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 10856.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08525
#9: Protein/peptide Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol-cytochrome c reductase complex 7.3 kDa protein


Mass: 6535.484 Da / Num. of mol.: 1 / Fragment: UNP residues 2-58 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22289

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Protein/peptide , 4 types, 4 molecules CDJK

#3: Protein/peptide Cytochrome b / / Complex III subunit 3 / Complex III subunit CYTB / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Cytochrome b-c1 complex subunit CYTB / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 43686.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00163
#4: Protein/peptide Cytochrome c1, heme protein, mitochondrial / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27807.395 Da / Num. of mol.: 1 / Fragment: UNP residues 62-309 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07143
#10: Protein/peptide Igh protein


Mass: 14365.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh / Production host: Escherichia coli (E. coli) / References: UniProt: Q53VQ5*PLUS
#11: Protein/peptide Ig kappa chain V-V region HP 124E1


Mass: 11926.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01647*PLUS

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Non-polymers , 7 types, 11 molecules

#12: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent *YM
#13: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H77O8P / Phosphatidic acid
#14: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#15: Chemical ChemComp-AOQ / 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / Atovaquone


Mass: 366.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19ClO3 / Atovaquone
#16: Chemical ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid *YM
#17: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H60O4
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: polyethylene glycol 4000, DMSO, Sucrose, Potassium phosphate, n-undecyl-?-D-maltopyranoside, atovaquone

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→25 Å / Num. obs: 77221 / % possible obs: 98.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 97.24 Å2 / Net I/σ(I): 15.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.04 Å24.9 Å
Translation3.04 Å24.9 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PHASERphenix: 1.8_1069phasing
PHENIX(phenix.refine: 1.8_1069)refinement
Coot0.6.2model building
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→24.989 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.2 / Stereochemistry target values: ML
Details: Author states that the structure was determined by molecular replacement and used the high-resolution structure of yeast cyt bc1 complex (pdb 3cx5) as basis for refinement. Quality of x-ray diffraction data for the new structure is limited and some poorly resolved loops were set to zero occupancy. The large complex covers a wide range of B-factors, with the highest in the matrix core subunits (chains A and B) and the lowest in the membrane integral subunit cytochrome b (chain C). In former structures obtained at room-temperature , such as 2KB9 at 2.3 angstrom, B factors range from above140 for chain A to below 30 for chain C. In this structure, the overall B-factors are lower but cover a similar range with very low up to zero B factors in the best ordered regions.
RfactorNum. reflection% reflection
Rfree0.2966 2005 2.6 %
Rwork0.2683 75090 -
Obs0.2691 77095 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.91 Å2 / Biso mean: 45.1046 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.04→24.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17279 0 367 0 17646
Biso mean--16.15 --
Num. residues----2147
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.01118113
f_angle_d1.47224609
f_chiral_restr0.092679
f_plane_restr0.0063113
f_dihedral_angle_d18.9416565
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.04-3.11590.45371430.41575390553399
3.1159-3.20.3741420.37095330547299
3.2-3.2940.38071430.35145305544898
3.294-3.40.36571420.33035353549598
3.4-3.52120.44761410.3655300544197
3.5212-3.66180.42641400.37735217535797
3.6618-3.82790.39061440.3325394553899
3.8279-4.02890.34291400.30045244538497
4.0289-4.28020.32041410.28815285542698
4.2802-4.60870.27111450.25665433557899
4.6087-5.0690.29951440.24225368551299
5.069-5.79460.25641450.242954435588100
5.7946-7.27060.23581460.250254835629100
7.2706-24.99010.2291490.198855455694100

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