+Open data
-Basic information
Entry | Database: PDB / ID: 6giq | ||||||
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Title | Saccharomyces cerevisiae respiratory supercomplex III2IV | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Respiratory chain / supercomplex / bc1 complex / cytochrome c oxidase | ||||||
Function / homology | Function and homology information matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / 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 / enzyme regulator activity / ATP synthesis coupled electron transport / proton transmembrane transport / nuclear periphery / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae W303 (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å | ||||||
Authors | Rathore, S. / Berndtsson, J. / Conrad, J. / Ott, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6giq.cif.gz | 980.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6giq.ent.gz | 816 KB | Display | PDB format |
PDBx/mmJSON format | 6giq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6giq_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6giq_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6giq_validation.xml.gz | 156.9 KB | Display | |
Data in CIF | 6giq_validation.cif.gz | 238.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6giq ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6giq | HTTPS FTP |
-Related structure data
Related structure data | 0004MC 0005C 0006C 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 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) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07256 #2: Protein | Mass: 40528.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07257 #5: Protein | Mass: 23393.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase #6: Protein | Mass: 17276.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00127 #7: Protein | Mass: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00128 #8: Protein | Mass: 10987.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08525 #9: Protein | Mass: 7485.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P22289 #10: Protein | Mass: 8602.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P37299 |
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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) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00163 #4: Protein | Mass: 34097.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07143 |
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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) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00401, cytochrome-c oxidase |
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#12: Protein | Mass: 28585.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00410, cytochrome-c oxidase |
#13: Protein | Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00420, cytochrome-c oxidase |
#14: Protein | Mass: 17164.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04037, cytochrome-c oxidase |
#16: Protein | Mass: 17366.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00427, cytochrome-c oxidase |
#17: Protein | Mass: 6942.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10174, cytochrome-c oxidase |
#19: Protein | Mass: 6974.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07255, cytochrome-c oxidase |
#20: Protein | Mass: 9799.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01519, cytochrome-c oxidase |
#21: Protein | Mass: 15046.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32799, cytochrome-c oxidase |
-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) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00424, cytochrome-c oxidase |
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#18: Protein | Mass: 8921.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04039, cytochrome-c oxidase |
-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) Saccharomyces cerevisiae W303 (yeast) |
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-Non-polymers , 13 types, 26 molecules
#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 |
-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 |
-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 |
Image recording | Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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 |