+Open data
-Basic information
Entry | Database: PDB / ID: 1kb9 | ||||||
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Title | YEAST CYTOCHROME BC1 COMPLEX | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / oxidoreductase / ubiquinone / stigmatellin / cardiolipin / phosphatidylinositol / phosphatidylcholin / phosphatidylethanolamin / undecyl-maltopyranoside / OXIDOREDUCTASE-ELECTRON TRANSPORT 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 / mitochondrial crista / aerobic respiration / nuclear periphery / proton transmembrane transport / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Lange, C. / Nett, J.H. / Trumpower, B.L. / Hunte, C. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: SPECIFIC ROLES OF PROTEIN-PHOSPHOLIPID INTERACTIONS IN THE YEAST CYTOCHROME BC1 COMPLEX STRUCTURE Authors: Lange, C. / Nett, J.H. / Trumpower, B.L. / Hunte, C. #1: Journal: Structure / Year: 2000 Title: Structure Of The Yeast Cytochrome Bc1 Complex Co-Crystallized With An Antibody Fv-Fragment Authors: Hunte, C. / Koepke, J. / Lange, C. / Rossmanith, T. / Michel, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kb9.cif.gz | 477.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kb9.ent.gz | 371.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kb9_validation.pdf.gz | 989.9 KB | Display | wwPDB validaton report |
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Full document | 1kb9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1kb9_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 1kb9_validation.cif.gz | 77.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kb9 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kb9 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ... , 6 types, 6 molecules ABFGHI
#1: Protein | Mass: 47445.242 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P07256, quinol-cytochrome-c reductase |
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#2: Protein | Mass: 38751.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P07257, quinol-cytochrome-c reductase |
#6: Protein | Mass: 8854.792 Da / Num. of mol.: 1 / Fragment: RESIDUES 74-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P00127, quinol-cytochrome-c reductase |
#7: Protein | Mass: 14355.443 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P00128, quinol-cytochrome-c reductase |
#8: Protein | Mass: 10856.314 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P08525, quinol-cytochrome-c reductase |
#9: Protein | Mass: 6301.232 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-58 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P22289, quinol-cytochrome-c reductase |
-Protein , 3 types, 3 molecules CDE
#3: Protein | Mass: 43674.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P00163 |
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#4: Protein | Mass: 27521.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 62-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P07143 |
#5: Protein | Mass: 20122.955 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Organelle: MITOCHONDRIA / References: UniProt: P08067, quinol-cytochrome-c reductase |
-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) / Production host: Escherichia coli (E. coli) |
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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) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 |
-Non-polymers , 10 types, 333 molecules
#12: Chemical | ChemComp-PCF / | ||||||||||||||
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#13: Chemical | ChemComp-UMQ / | ||||||||||||||
#14: Chemical | #15: Chemical | ChemComp-SMA / | #16: Chemical | ChemComp-UQ6 / | #17: Chemical | ChemComp-PIE / | #18: Chemical | #19: Chemical | ChemComp-CDL / | #20: Chemical | ChemComp-FES / | #21: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.83 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG4000, pH 8, VAPOR DIFFUSION, SITTING DROP |
Crystal grow | *PLUS Method: unknown / Details: Hunte, C., (2000) Structure, 8, 669. |
-Data collection
Detector | Type: MARRESEARCH / Detector: CCD |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→14.96 Å / Num. all: 168517 / Num. obs: 168517 / Observed criterion σ(F): 0 / Biso Wilson estimate: 31.9 Å2 / Limit h max: 82 / Limit h min: -93 / Limit k max: 71 / Limit k min: -93 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 3621196.32 / Observed criterion F min: 18.17 |
Reflection | *PLUS Highest resolution: 2.3 Å |
-Processing
Software |
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Refinement | Resolution: 2.3→14.96 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 38.6265 Å2 / ksol: 0.273859 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.38 Å2 / Biso mean: 69.92 Å2 / Biso min: 20.92 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.96 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: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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