+Open data
-Basic information
Entry | Database: PDB / ID: 5z62 | ||||||||||||||||||
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Title | Structure of human cytochrome c oxidase | ||||||||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 14 | ||||||||||||||||||
Keywords | ELECTRON TRANSPORT / cytochrome c oxidase | ||||||||||||||||||
Function / homology | Function and homology information Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / regulation of oxidative phosphorylation / : / : / cytochrome-c oxidase ...Complex IV assembly / respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / regulation of oxidative phosphorylation / : / : / cytochrome-c oxidase / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / response to electrical stimulus / ATP synthesis coupled electron transport / enzyme regulator activity / Mitochondrial protein degradation / lactation / substantia nigra development / cerebellum development / generation of precursor metabolites and energy / central nervous system development / TP53 Regulates Metabolic Genes / mitochondrial membrane / Cytoprotection by HMOX1 / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / response to hypoxia / oxidoreductase activity / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / nucleoplasm / membrane / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Gu, J. / Zong, S. / Wu, M. / Yang, M. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Cell Res / Year: 2018 Title: Structure of the intact 14-subunit human cytochrome c oxidase. Authors: Shuai Zong / Meng Wu / Jinke Gu / Tianya Liu / Runyu Guo / Maojun Yang / Abstract: Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the ...Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the terminal enzyme of the electron transport chain, existing either as randomly scattered complexes or as a component of supercomplexes. NDUFA4 was previously assumed as a subunit of complex-I, but recent biochemical data suggested it may be a subunit of complex-IV. However, no structural evidence supporting this notion was available till now. Here we obtained the 3.3 Å resolution structure of complex-IV derived from the human supercomplex IIIIIV and assigned the NDUFA4 subunit into complex-IV. Intriguingly, NDUFA4 lies exactly at the dimeric interface observed in previously reported crystal structures of complex-IV homodimer which would preclude complex-IV dimerization. Combining previous structural and biochemical data shown by us and other groups, we propose that the intact complex-IV is a monomer containing 14 subunits. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5z62.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z62.ent.gz | 283.2 KB | Display | PDB format |
PDBx/mmJSON format | 5z62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z62_validation.pdf.gz | 1009.2 KB | Display | wwPDB validaton report |
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Full document | 5z62_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5z62_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 5z62_validation.cif.gz | 86.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z62 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z62 | HTTPS FTP |
-Related structure data
Related structure data | 6896MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome c oxidase subunit ... , 14 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | Mass: 57076.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00395, cytochrome-c oxidase |
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#2: Protein | Mass: 25580.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00403 |
#3: Protein | Mass: 29844.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00414 |
#4: Protein | Mass: 16890.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13073 |
#5: Protein | Mass: 12517.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20674 |
#6: Protein | Mass: 10627.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10606 |
#7: Protein | Mass: 8691.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12074 |
#8: Protein | Mass: 9757.906 Da / Num. of mol.: 1 / Fragment: UNP residues 5-86 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14854 |
#9: Protein | Mass: 8596.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09669 |
#10: Protein | Mass: 6196.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14406 |
#11: Protein/peptide | Mass: 5488.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24311 |
#12: Protein/peptide | Mass: 5363.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15954 |
#13: Protein/peptide | Mass: 4769.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10176 |
#14: Protein | Mass: 9137.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00483 |
-Non-polymers , 6 types, 11 molecules
#15: Chemical | #16: Chemical | ChemComp-MG / | #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-CDL / | #20: Chemical | ChemComp-ZN / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human cytochrome c oxidase / Type: COMPLEX / Details: 14 subunits / Entity ID: #1-#14 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1010000 / Symmetry type: POINT |