+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6896 | |||||||||
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Title | Structure of human cytochrome c oxidase | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information oxidoreduction-driven active transmembrane transporter activity / : / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / : / regulation of oxidative phosphorylation / : / cytochrome-c oxidase ...oxidoreduction-driven active transmembrane transporter activity / : / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / respiratory gaseous exchange by respiratory system / : / regulation of oxidative phosphorylation / : / cytochrome-c oxidase / : / oxidative phosphorylation / response to copper ion / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / generation of precursor metabolites and energy / electron transport coupled proton transport / Respiratory electron transport / enzyme regulator activity / ATP synthesis coupled electron transport / response to nutrient / response to electrical stimulus / substantia nigra development / lactation / proton transmembrane transport / respiratory electron transport chain / cerebellum development / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / central nervous system development / NADH dehydrogenase (ubiquinone) activity / TP53 Regulates Metabolic Genes / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / response to oxidative stress / membrane => GO:0016020 / response to hypoxia / electron transfer activity / mitochondrial inner membrane / 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 | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zong S / Wu M / Gu J / Yang M | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6896.map.gz | 19.8 MB | EMDB map data format | |
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Header (meta data) | emd-6896-v30.xml emd-6896.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_6896.png | 90.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6896 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6896 | HTTPS FTP |
-Validation report
Summary document | emd_6896_validation.pdf.gz | 303 KB | Display | EMDB validaton report |
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Full document | emd_6896_full_validation.pdf.gz | 302.5 KB | Display | |
Data in XML | emd_6896_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6896 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6896 | HTTPS FTP |
-Related structure data
Related structure data | 5z62MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6896.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : intact 14-subunit human cytochrome c oxidase
Entire | Name: intact 14-subunit human cytochrome c oxidase |
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Components |
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-Supramolecule #1: intact 14-subunit human cytochrome c oxidase
Supramolecule | Name: intact 14-subunit human cytochrome c oxidase / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.56 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1010000 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |