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Open data
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Basic information
Entry | Database: PDB / ID: 2occ | ||||||
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Title | BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE | ||||||
![]() | (CYTOCHROME C ...) x 13 | ||||||
![]() | OXIDOREDUCTASE / CYTOCHROME(C)-OXYGEN / CYTOCHROME C OXIDASE | ||||||
Function / homology | ![]() 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 / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / membrane => GO:0016020 / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsukihara, T. / Yao, M. | ||||||
![]() | ![]() Title: Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Authors: Yoshikawa, S. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yamashita, E. / Inoue, N. / Yao, M. / Fei, M.J. / Libeu, C.P. / Mizushima, T. / Yamaguchi, H. / Tomizaki, T. / Tsukihara, T. #1: ![]() 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. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 703.7 KB | Display | ![]() |
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PDB format | ![]() | 583.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 733 KB | Display | ![]() |
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Full document | ![]() | 797 KB | Display | |
Data in XML | ![]() | 72.8 KB | Display | |
Data in CIF | ![]() | 112.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ocoC ![]() 1ocrC ![]() 1oczC ![]() 1occS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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, NA, AND ZN. THE SIDE CHAINS OF H 240 AND Y244 OF MOLECULES A AND N ARE LINKED TOGETHER BY A COVALENT BOND. THE ELECTRON DENSITY OF REGION FROM D(Q) 1 TO D(Q) 3, E(R) 1 TO E(R) 4, H(U) 1 TO H(U) 6, J(W) 59, K(X) 1 TO K(X) 5, K(X) 53 TO K(X) 54 AND M(Z) 41 TO M(Z) 43 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. | |
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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 HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #2: Protein | Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() References: UniProt: P00404, UniProt: P68530*PLUS, 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 HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #7: Protein | Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG, NA AND ZN. Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 18 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/ZN.gif)
#14: Chemical | ChemComp-CU / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-HEA / #18: Chemical | #19: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % Description: OSCILLATION METHOD, DATA COLLECTION ON MULTIPLE DATES: 16,19,29,30-MAY-1996, 18-MAY-1995, 04-DEC-1994 |
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Crystal grow | pH: 6.8 / Details: pH 6.8 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 284634 / % possible obs: 90.2 % / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 38.81 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 4.1 / % possible all: 89.9 |
Reflection | *PLUS Num. measured all: 973307 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 89.9 % / Num. unique obs: 28157 / Num. measured obs: 90077 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OCC Resolution: 2.3→15 Å / Rfactor Rfree error: 0.0022 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.22 / Rfactor Rfree: 0.253 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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