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Open data
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Basic information
| Entry | Database: PDB / ID: 36cv | |||||||||
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| Title | Crystal structure of cyanate bound bovine cytochrome c oxidase | |||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | |||||||||
Keywords | MEMBRANE PROTEIN / Bioenergetics / Proton translocation / OXIDOREDUCTASE | |||||||||
| Function / homology | Function and homology informationComplex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / Mitochondrial translation termination / cytochrome-c oxidase ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / Mitochondrial translation termination / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / oxidative phosphorylation / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / mitochondrial membrane / protein-macromolecule adaptor activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Ishigami, I. / Rousseau, D.L. / Yeh, S.-R. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: J Porphyr Phthalocyanines / Year: 2026Title: A cyanate-bridged binuclear center in bovine cytochrome c oxidase Authors: Ishigami, I. / Yeh, S.R. / Rousseau, D.L. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 36cv.cif.gz | 840.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb36cv.ent.gz | 663.2 KB | Display | PDB format |
| PDBx/mmJSON format | 36cv.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/6c/36cv ftp://data.pdbj.org/pub/pdb/validation_reports/6c/36cv | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 36ezC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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| Unit cell |
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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 natural source / Source: (natural) ![]() #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 1 types, 6 molecules 
| #26: Sugar | ChemComp-DMU / |
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-Non-polymers , 16 types, 1260 molecules 






























| #14: Chemical | | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-PGV / ( #18: Chemical | ChemComp-HEA / #19: Chemical | ChemComp-EDO / #20: Chemical | ChemComp-0NM / #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CHD / #24: Chemical | ChemComp-PEK / ( #25: Chemical | ChemComp-CDL / #27: Chemical | ChemComp-TGL / #28: Chemical | #29: Chemical | #30: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.34 % |
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| Crystal grow | Temperature: 277 K / Method: batch mode / Details: PEG 4000, Potassium Phosphate, Decylmaltoside |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2021 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
| Reflection | Resolution: 2.1→29.997 Å / Num. obs: 393869 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 10.7 |
| Reflection shell | Resolution: 2.1→2.154 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 25627 / CC1/2: 0.51 / % possible all: 99.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.997 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.937 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.143 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 48.239 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.1→29.997 Å
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| Refine LS restraints |
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| LS refinement shell |
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About Yorodumi





X-RAY DIFFRACTION
United States, 2items
Citation
PDBj





