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Open data
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Basic information
Entry | Database: PDB / ID: 6giq | ||||||
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Title | Saccharomyces cerevisiae respiratory supercomplex III2IV | ||||||
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![]() | ELECTRON TRANSPORT / Respiratory chain / supercomplex / bc1 complex / cytochrome c oxidase | ||||||
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: 3.23 Å | ||||||
![]() | Rathore, S. / Berndtsson, J. / Conrad, J. / Ott, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the yeast respiratory supercomplex. Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott / ![]() Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 980.3 KB | Display | ![]() |
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PDB format | ![]() | 816 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 | ![]() | 156.9 KB | Display | |
Data in CIF | ![]() | 238.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0004MC ![]() 0005C ![]() 0006C 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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Components
-Cytochrome b-c1 complex subunit ... , 8 types, 16 molecules ALBMEPFQGRHSITUV
#1: Protein | Mass: 50282.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 40528.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 23393.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 17276.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 10987.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 7485.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 8602.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 2 types, 4 molecules CNDO
#3: Protein | Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 34097.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome c oxidase subunit ... , 9 types, 9 molecules abcdfgijk
#11: Protein | Mass: 58832.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#12: Protein | Mass: 28585.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 17164.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 17366.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 6942.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 6974.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 9799.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 15046.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Cytochrome c oxidase polypeptide ... , 2 types, 2 molecules eh
#15: Protein | Mass: 17161.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#18: Protein | Mass: 8921.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules m
#22: Protein/peptide | Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 13 types, 26 molecules ![](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/7PH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/9PE.gif)
![](data/chem/img/CN3.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/8PE.gif)
![](data/chem/img/CN5.gif)
![](data/chem/img/UQ6.gif)
![](data/chem/img/7PH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/9PE.gif)
![](data/chem/img/CN3.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CUA.gif)
#23: Chemical | #24: Chemical | ChemComp-HEM / #25: Chemical | #26: Chemical | ChemComp-CN5 / ( | #27: Chemical | #28: Chemical | #29: Chemical | #30: Chemical | #31: Chemical | #32: Chemical | ChemComp-CN3 / ( | #33: Chemical | ChemComp-CU / | #34: Chemical | #35: Chemical | ChemComp-CUA / | |
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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
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Source (natural) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203271 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Cross-Correlation coefficient |