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Yorodumi- PDB-4pd4: Structural analysis of atovaquone-inhibited cytochrome bc1 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pd4 | |||||||||
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Title | Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/INHIBITOR / Cytochrome bc1 complex / Membrane protein complex / antimalarial drug / inhibitor / OXIDOREDUCTASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information : / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity ...: / Complex III assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cellular respiration / mitochondrial electron transport, ubiquinol to cytochrome c / immunoglobulin complex / mitochondrial crista / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / adaptive immune response / mitochondrial inner membrane / oxidoreductase activity / immune response / heme binding / mitochondrion / proteolysis / extracellular space / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 Å | |||||||||
Authors | Birth, D. / Kao, W.-C. / Hunte, C. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pd4.cif.gz | 466.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pd4.ent.gz | 363.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pd4_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4pd4_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 4pd4_validation.xml.gz | 88.2 KB | Display | |
Data in CIF | 4pd4_validation.cif.gz | 116.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/4pd4 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/4pd4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Cytochrome b-c1 complex subunit ... , 7 types, 7 molecules ABEFGHI
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 | 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 | 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 |
-Protein , 2 types, 2 molecules CD
#3: Protein | 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 |
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#4: Protein | 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 |
-Antibody , 2 types, 2 molecules JK
#10: Antibody | 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 |
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#11: Antibody | 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 |
-Non-polymers , 7 types, 11 molecules
#12: Chemical | ChemComp-UMQ / | ||||||||||
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#13: Chemical | #14: Chemical | #15: Chemical | ChemComp-AOQ / | #16: Chemical | ChemComp-3PE / | #17: Chemical | ChemComp-UQ6 / | #18: Chemical | ChemComp-FES / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.96 % |
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Crystal grow | Temperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: polyethylene glycol 4000, DMSO, Sucrose, Potassium phosphate, n-undecyl-?-D-maltopyranoside, atovaquone |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method 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 ...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.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.91 Å2 / Biso mean: 45.1046 Å2 / Biso min: 0 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.04→24.989 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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