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Yorodumi- PDB-7tih: Structure of oxidized bovine cytochrome c oxidase with reduced me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tih | |||||||||||||||
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Title | Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure | |||||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Bioenergetics / Proton translocation / OXIDOREDUCTASE | |||||||||||||||
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 / cytochrome-c oxidase activity / electron transport coupled proton transport / 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: 2.35 Å | |||||||||||||||
Authors | Ishigami, I. / Rousseau, D.L. / Yeh, S.-R. / Russi, S. / Cohen, A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase. Authors: Ishigami, I. / Russi, S. / Cohen, A. / Yeh, S.R. / Rousseau, D.L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tih.cif.gz | 849.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tih.ent.gz | 671 KB | Display | PDB format |
PDBx/mmJSON format | 7tih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/7tih ftp://data.pdbj.org/pub/pdb/validation_reports/ti/7tih | HTTPS FTP |
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-Related structure data
Related structure data | 7thuC 7tieSC 7tiiC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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) 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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 |
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-Sugars , 1 types, 6 molecules
#26: Sugar | ChemComp-DMU / |
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-Non-polymers , 16 types, 1667 molecules
#14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-PGV / ( #18: Chemical | ChemComp-HEA / #19: Chemical | ChemComp-EDO / #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-TGL / #23: Chemical | #24: Chemical | ChemComp-CHD / #25: Chemical | ChemComp-CDL / #27: Chemical | ChemComp-PEK / ( #28: Chemical | #29: Chemical | #30: 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: 69.86 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 / 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: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→39.339 Å / Num. obs: 277487 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.993 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.35→2.48 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 40279 / CC1/2: 0.456 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TIE Resolution: 2.35→39.339 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.166 / SU B: 9.618 / SU ML: 0.201 / Average fsc free: 0.82 / Average fsc work: 0.8341 / Cross valid method: FREE R-VALUE / ESU R: 0.229 / ESU R Free: 0.198 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: 45.597 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→39.339 Å
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Refine LS restraints |
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LS refinement shell |
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