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Open data
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Basic information
Entry | Database: PDB / ID: 6ymx | |||||||||||||||
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Title | CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae | |||||||||||||||
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![]() | ELECTRON TRANSPORT / Complex / CIII / CIV / Supercomplex | |||||||||||||||
Function / homology | ![]() matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||||||||
![]() | Berndtsson, J. / Rathore, S. / Ott, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 866.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 166.9 KB | Display | |
Data in CIF | ![]() | 250.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10847MC ![]() 6ymyC M: map data used to model this data 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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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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() References: UniProt: P04037 |
#5: Protein | Mass: 14324.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00424 |
#6: Protein | Mass: 11725.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00427 |
#7: Protein | Mass: 6410.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P10174 |
#8: Protein | Mass: 5737.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P04039 |
#9: Protein | Mass: 6241.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P07255 |
#10: Protein | Mass: 9225.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q01519 |
#11: Protein | Mass: 13306.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P32799 |
#12: Protein/peptide | Mass: 4347.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q2V2P9 |
-Cytochrome b-c1 complex subunit ... , 11 types, 16 molecules ALBMEPFGRHSIQTUV
#13: Protein | Mass: 47459.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P07256 #14: Protein | Mass: 38751.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P07257 #17: Protein | Mass: 20122.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P08067, quinol-cytochrome-c reductase #18: Protein | | Mass: 8854.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00127 #19: Protein | Mass: 14452.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00128 #20: Protein | Mass: 10856.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P08525 #21: Protein | | Mass: 6214.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P22289 #22: Protein | | Mass: 8983.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00127 #23: Protein | | Mass: 6230.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P22289 #24: Protein/peptide | | Mass: 4920.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P37299 #25: Protein | | Mass: 5750.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P37299 |
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-Protein , 2 types, 4 molecules CNDO
#15: Protein | Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P00163, quinol-cytochrome-c reductase #16: Protein | Mass: 27807.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P07143, quinol-cytochrome-c reductase |
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-Non-polymers , 15 types, 38 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/CN3.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/6PH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/8PE.gif)
![](data/chem/img/CN5.gif)
![](data/chem/img/UQ6.gif)
![](data/chem/img/9PE.gif)
![](data/chem/img/7PH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/CN3.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/6PH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/8PE.gif)
![](data/chem/img/CN5.gif)
![](data/chem/img/UQ6.gif)
![](data/chem/img/9PE.gif)
![](data/chem/img/7PH.gif)
![](data/chem/img/FES.gif)
#26: Chemical | ChemComp-CU / | ||||||||||||||||||||||||||
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#27: Chemical | #28: Chemical | ChemComp-PTY / #29: Chemical | #30: Chemical | ChemComp-CUA / | #31: Chemical | ChemComp-PCF / #32: Chemical | ChemComp-ZN / | #33: Chemical | #34: Chemical | ChemComp-HEM / #35: Chemical | #36: Chemical | ChemComp-CN5 / ( | #37: Chemical | #38: Chemical | #39: Chemical | #40: Chemical | |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Respiratroy supercopmlex CIII2/CIV / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL | |||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() 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 |
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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: ![]() |
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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 647805 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201223 / Num. of class averages: 1 / Symmetry type: POINT |