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Yorodumi- PDB-1occ: STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDI... -
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-Basic information
Entry | Database: PDB / ID: 1occ | ||||||
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Title | STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE | ||||||
Components | (CYTOCHROME C ...) x 13 | ||||||
Keywords | OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN) / CYTOCHROME C OXIDASE | ||||||
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 / Resolution: 2.8 Å | ||||||
Authors | Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S. | ||||||
Citation | Journal: Science / Year: 1996 Title: The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S. #1: Journal: Science / Year: 1995 Title: Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1occ.cif.gz | 696.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1occ.ent.gz | 585.1 KB | Display | PDB format |
PDBx/mmJSON format | 1occ.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1occ_validation.pdf.gz | 726.1 KB | Display | wwPDB validaton report |
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Full document | 1occ_full_validation.pdf.gz | 812.8 KB | Display | |
Data in XML | 1occ_validation.xml.gz | 75.3 KB | Display | |
Data in CIF | 1occ_validation.cif.gz | 114 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1occ ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1occ | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99386, -0.001, 0.11065), Vector: Details | THIS ENZYME IS A MULTI-COMPONENT PROTEIN COMPLEX AND IS A HOMODIMER. EACH MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS: HEME A, HEME A3, CUA, CUB, MG, AND ZN. THE DEPOSITOR PROVIDED THE COORDINATES OF ONE MONOMER. THE PDB GENERATED THE OTHER MONOMER FROM THE MONOMER THAT WAS DEPOSITED USING THE TRANSFORMATION PROVIDED BY THE DEPOSITOR. | |
-Components
-CYTOCHROME C ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ
#1: Protein | Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00396, cytochrome-c oxidase #2: Protein | Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P68530, cytochrome-c oxidase #3: Protein | Mass: 29943.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00415, cytochrome-c oxidase #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00423, cytochrome-c oxidase #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00426, cytochrome-c oxidase #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00428, cytochrome-c oxidase #7: Protein | Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07471, cytochrome-c oxidase #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00429, cytochrome-c oxidase #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P04038, cytochrome-c oxidase #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07470, cytochrome-c oxidase #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13183, cytochrome-c oxidase #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00430, cytochrome-c oxidase #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P10175, cytochrome-c oxidase |
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-Non-polymers , 4 types, 14 molecules
#14: Chemical | ChemComp-CU / #15: Chemical | #16: Chemical | ChemComp-HEA / #17: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.64 % / Description: OSCILLATION METHOD | |||||||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.8 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 155505 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.78 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 69.6 |
Reflection shell | *PLUS % possible obs: 69.6 % |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 1 Details: THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES. THE ...Details: THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES. THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES.
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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