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Yorodumi- PDB-8h8r: Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h8r | |||||||||||||||
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Title | Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxidized State | |||||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||
Keywords | OXIDOREDUCTASE / Calcium / Fully Oxidized | |||||||||||||||
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: 1.7 Å | |||||||||||||||
Authors | Muramoto, K. / Shinzawa-Itoh, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2023 Title: Calcium-bound structure of bovine cytochrome c oxidase. Authors: Muramoto, K. / Shinzawa-Itoh, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h8r.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8h8r.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8h8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h8r_validation.pdf.gz | 19.8 MB | Display | wwPDB validaton report |
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Full document | 8h8r_full_validation.pdf.gz | 19.8 MB | Display | |
Data in XML | 8h8r_validation.xml.gz | 176.6 KB | Display | |
Data in CIF | 8h8r_validation.cif.gz | 232.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h8r ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h8r | HTTPS FTP |
-Related structure data
Related structure data | 8h8sC 7cohS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ
#1: Protein | Mass: 57093.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: MT-CO1, COI, COXI, MTCO1 / Production host: Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: MT-CO2, COII, COX2, COXII, MTCO2 / Production host: Bos taurus (cattle) / References: UniProt: P68530, cytochrome-c oxidase #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: MT-CO3, COIII, COXIII, MTCO3 / Production host: Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX4I1, COX4 / Production host: Bos taurus (cattle) / References: UniProt: P00423 #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX5A / Production host: Bos taurus (cattle) / References: UniProt: P00426 #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX5B / Production host: Bos taurus (cattle) / References: UniProt: P00428 #7: Protein | Mass: 9549.802 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6A2, COX6A / Production host: Bos taurus (cattle) / References: UniProt: P07471 #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6B1, COX6B / Production host: Bos taurus (cattle) / References: UniProt: P00429 #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX6C / Production host: Bos taurus (cattle) / References: UniProt: P04038 #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7A1, COX7A, COX7AH / Production host: Bos taurus (cattle) / References: UniProt: P07470 #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7B / Production host: Bos taurus (cattle) / References: UniProt: P13183 #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX7C, COX7CP1 / Production host: Bos taurus (cattle) / References: UniProt: P00430 #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: COX8B, COX8H / Production host: Bos taurus (cattle) / References: UniProt: P10175 |
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-Sugars , 1 types, 42 molecules
#20: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 2098 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-LFA / #21: Chemical | ChemComp-EDO / #22: Chemical | ChemComp-PGV / ( #23: Chemical | #24: Chemical | ChemComp-CHD / #25: Chemical | #26: Chemical | ChemComp-CDL / #27: Chemical | #28: Chemical | #29: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 4.08 Å3/Da / Density % sol: 69.85 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 Details: 40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→200 Å / Num. obs: 691219 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 32.1 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.085 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 104230 / CC1/2: 0.78 / Rrim(I) all: 1.38 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7COH Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.781 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.188 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→40 Å
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