+Open data
-Basic information
Entry | Database: PDB / ID: 6ymy | |||||||||||||||
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Title | Cytochrome c oxidase from Saccharomyces cerevisiae | |||||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 12 | |||||||||||||||
Keywords | ELECTRON TRANSPORT / CIV / CytcO | |||||||||||||||
Function / homology | Function and homology information mitochondrial cytochrome c oxidase assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / cytochrome-c oxidase / : / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / cytochrome-c oxidase / : / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / zinc ion binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
Authors | Berndtsson, J. / Rathore, S. / Ott, M. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: EMBO Rep / Year: 2020 Title: Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. Authors: Jens Berndtsson / Andreas Kohler / Sorbhi Rathore / Lorena Marin-Buera / Hannah Dawitz / Jutta Diessl / Verena Kohler / Antoni Barrientos / Sabrina Büttner / Flavia Fontanesi / Martin Ott / Abstract: Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in ...Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms. | |||||||||||||||
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 | 6ymy.cif.gz | 331 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ymy.ent.gz | 273.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ymy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ymy_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6ymy_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ymy_validation.xml.gz | 67.4 KB | Display | |
Data in CIF | 6ymy_validation.cif.gz | 97.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/6ymy ftp://data.pdbj.org/pub/pdb/validation_reports/ym/6ymy | HTTPS FTP |
-Related structure data
Related structure data | 10848MC 6ymxC C: citing same article (ref.) M: map data used to model this data |
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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 ... , 12 types, 12 molecules abcdefghijkm
#1: Protein | Mass: 58316.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P00401, cytochrome-c oxidase |
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#2: Protein | Mass: 26779.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P00410, cytochrome-c oxidase |
#3: Protein | Mass: 30252.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P00420, cytochrome-c oxidase |
#4: Protein | Mass: 12694.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P04037 |
#5: Protein | Mass: 14324.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P00424 |
#6: Protein | Mass: 11725.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P00427 |
#7: Protein | Mass: 6410.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P10174 |
#8: Protein | Mass: 5737.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P04039 |
#9: Protein | Mass: 6056.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P07255 |
#10: Protein | Mass: 9225.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q01519 |
#11: Protein | Mass: 13306.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32799 |
#12: Protein/peptide | Mass: 4347.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q2V2P9 |
-Non-polymers , 7 types, 16 molecules
#13: Chemical | ChemComp-CU / | ||||||||||
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#14: Chemical | #15: Chemical | ChemComp-PTY / #16: Chemical | ChemComp-CN3 / ( | #17: Chemical | ChemComp-CUA / | #18: Chemical | #19: Chemical | ChemComp-ZN / | |
-Details
Has ligand of interest | N |
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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: Cytochrome c oxidase / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: W303-1b / Organelle: Mitochondria | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: -3 nm / Nominal defocus min: -1.4 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8775 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 647805 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201223 / Num. of class averages: 1 / Symmetry type: POINT |