+Open data
-Basic information
Entry | Database: PDB / ID: 2ibz | |||||||||
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Title | Yeast Cytochrome BC1 Complex with Stigmatellin | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / multisubunit membrane protein complex | |||||||||
Function / homology | Function and homology information Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade ...Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / matrix side of mitochondrial inner membrane / FCERI mediated Ca+2 mobilization / protein processing involved in protein targeting to mitochondrion / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / Regulation of actin dynamics for phagocytic cup formation / Mitochondrial protein degradation / : / immunoglobulin complex / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / immunoglobulin mediated immune response / proton transmembrane transport / nuclear periphery / antigen binding / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / extracellular region / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | |||||||||
Authors | Hunte, C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome bc(1) Complex. Authors: Lancaster, C.R. / Hunte, C. / Kelley, J. / Trumpower, B.L. / Ditchfield, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ibz.cif.gz | 452.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ibz.ent.gz | 370.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ibz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ibz_validation.pdf.gz | 753.6 KB | Display | wwPDB validaton report |
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Full document | 2ibz_full_validation.pdf.gz | 801.7 KB | Display | |
Data in XML | 2ibz_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 2ibz_validation.cif.gz | 72.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2ibz ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2ibz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Ubiquinol-cytochrome-c reductase complex core protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47445.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07256, quinol-cytochrome-c reductase |
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#2: Protein | Mass: 38751.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07257, 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00163, quinol-cytochrome-c reductase |
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#4: Protein | Mass: 27807.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07143, quinol-cytochrome-c reductase |
#5: Protein | Mass: 20122.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase |
-Ubiquinol-cytochrome c reductase complex ... , 4 types, 4 molecules HFGI
#6: Protein | Mass: 8854.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00127, quinol-cytochrome-c reductase |
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#7: Protein | Mass: 14583.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00128, quinol-cytochrome-c reductase |
#8: Protein | Mass: 10987.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08525, quinol-cytochrome-c reductase |
#9: Protein | Mass: 7485.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22289, quinol-cytochrome-c reductase |
-Antibody , 2 types, 2 molecules XY
#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: variable domain antibody heavy chain / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18531*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) / Gene: variable domain antibody light chain / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: A0N6Y3*PLUS |
-Non-polymers , 5 types, 346 molecules
#12: Chemical | #13: Chemical | ChemComp-UQ6 / | #14: Chemical | ChemComp-SMA / | #15: Chemical | ChemComp-FES / | #16: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 17 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: precipitant PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 |
Detector | Type: MARRESEARCH / Detector: CCD |
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: 199019 / Num. obs: 168517 / % possible obs: 84.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.2 / Num. unique all: 23537 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→14.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 69.9 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014
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