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Yorodumi- PDB-3ag3: Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ag3 | ||||||
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Title | Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully Reduced State at 100 K | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Copper / Electron transport / Formylation / Heme / Iron / Membrane / Mitochondrion / Mitochondrion inner membrane / Respiratory chain / Transmembrane / Transport / Acetylation / Transit peptide / Zinc / Isopeptide bond / Ubl conjugation | ||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / enzyme regulator activity / ATP synthesis coupled electron transport / central nervous system development / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Muramoto, K. / Ohta, K. / Shinzawa-Itoh, K. / Kanda, K. / Taniguchi, M. / Nabekura, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate Authors: Muramoto, K. / Ohta, K. / Shinzawa-Itoh, K. / Kanda, K. / Taniguchi, M. / Nabekura, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ag3.cif.gz | 827.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ag3.ent.gz | 671.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ag3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ag3_validation.pdf.gz | 9.7 MB | Display | wwPDB validaton report |
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Full document | 3ag3_full_validation.pdf.gz | 10.1 MB | Display | |
Data in XML | 3ag3_validation.xml.gz | 211.8 KB | Display | |
Data in CIF | 3ag3_validation.cif.gz | 260.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3ag3 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3ag3 | HTTPS FTP |
-Related structure data
Related structure data | 3ag1C 3ag2C 3ag4C 8ijnC 2eijS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Cytochrome c oxidase subunit ... , 12 types, 24 molecules ANBOCPDQERFSGTHUIVKXLYMZ
#1: Protein | Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530, cytochrome-c oxidase #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423, cytochrome-c oxidase #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426, cytochrome-c oxidase #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428, cytochrome-c oxidase #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471, cytochrome-c oxidase #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429, cytochrome-c oxidase #9: Protein | Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038, cytochrome-c oxidase #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183, cytochrome-c oxidase #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430, cytochrome-c oxidase #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175, cytochrome-c oxidase |
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-Protein / Sugars , 2 types, 6 molecules JW
#10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470, cytochrome-c oxidase #28: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 1795 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-TGL / #20: Chemical | ChemComp-PGV / ( #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CHD / #24: Chemical | #25: Chemical | ChemComp-PEK / ( #26: Chemical | ChemComp-CDL / #27: Chemical | #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.13 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Date: Dec 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→83.6 Å / Num. obs: 617758 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EIJ Resolution: 1.8→40 Å
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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