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Yorodumi- PDB-3abl: Bovine heart cytochrome c oxidase at the fully oxidized state (15... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3abl | ||||||
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Title | Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) | ||||||
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 / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Aoyama, H. / Muramoto, K. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Ogura, T. / Yoshikawa, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump Authors: Aoyama, H. / Muramoto, K. / Shinzawa-Itoh, K. / Hirata, K. / Yamashita, E. / Tsukihara, T. / Ogura, 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 | 3abl.cif.gz | 818.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3abl.ent.gz | 666 KB | Display | PDB format |
PDBx/mmJSON format | 3abl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3abl ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3abl | HTTPS FTP |
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-Related structure data
Related structure data | 2zxwC 3abmC 2dyrS 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 #24: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 1760 molecules
#14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-HEA / #19: Chemical | ChemComp-TGL / #20: Chemical | ChemComp-PGV / ( #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CHD / #25: Chemical | #26: Chemical | ChemComp-CDL / #27: Chemical | #28: Chemical | ChemComp-PEK / ( #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 201 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.36 % |
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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: Oct 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→56.8 Å / Num. obs: 390624 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DYR Resolution: 2.1→40 Å /
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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