+Open data
-Basic information
Entry | Database: PDB / ID: 5luf | ||||||
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Title | Cryo-EM of bovine respirasome | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Mitochondria / supercomplex / respiratory chain | ||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / : / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / : / cytochrome-c oxidase / : / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / electron transport coupled proton transport / : / enzyme regulator activity / ATP synthesis coupled electron transport / respiratory electron transport chain / central nervous system development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 Å | ||||||
Authors | Sousa, J.S. / Mills, D.J. / Vonck, J. / Kuehlbrandt, W. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Functional asymmetry and electron flow in the bovine respirasome. Authors: Joana S Sousa / Deryck J Mills / Janet Vonck / Werner Kühlbrandt / Abstract: Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex IIIIIV from bovine heart ...Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex IIIIIV from bovine heart mitochondria by cryo-EM at 9 Å resolution. Most protein-protein contacts between complex I, III and IV in the membrane are mediated by supernumerary subunits. Of the two Rieske iron-sulfur cluster domains in the complex III dimer, one is resolved, indicating that this domain is immobile and unable to transfer electrons. The central position of the active complex III monomer between complex I and IV in the respirasome is optimal for accepting reduced quinone from complex I over a short diffusion distance of 11 nm, and delivering reduced cytochrome to complex IV. The functional asymmetry of complex III provides strong evidence for directed electron flow from complex I to complex IV through the active complex III monomer in the mammalian supercomplex. | ||||||
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 | 5luf.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5luf.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5luf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5luf ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5luf | HTTPS FTP |
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-Related structure data
Related structure data | 4107MC 4108C 4109C 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 ... , 9 types, 18 molecules clmneqfrgshtiujvkw
#1: Protein | Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800 #2: Protein | Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004 #5: Protein | Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase #6: Protein | Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129 #7: Protein | Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271 #8: Protein | Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126 #9: Protein | Mass: 7964.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase #10: Protein | Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130 #11: Protein | Mass: 6370.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07552 |
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+Protein , 28 types, 30 molecules bodpABCDEFGHIJKLMNOPQSTVWXYaUZ
-Cytochrome c oxidase subunit ... , 13 types, 13 molecules xyz1234567890
#12: Protein | Mass: 57065.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase |
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#13: Protein | Mass: 26040.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530 |
#14: Protein | Mass: 29943.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415 |
#15: Protein | Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423 |
#16: Protein | Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426 |
#17: Protein | Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428 |
#18: Protein | Mass: 9452.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471 |
#19: Protein | Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429 |
#20: Protein | Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038 |
#21: Protein | Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470 |
#22: Protein | Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183 |
#23: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430 |
#24: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175 |
-Protein/peptide , 1 types, 1 molecules R
#42: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
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-Non-polymers , 8 types, 22 molecules
#52: Chemical | ChemComp-HEM / #53: Chemical | #54: Chemical | #55: Chemical | #56: Chemical | ChemComp-MG / | #57: Chemical | #58: Chemical | ChemComp-ZN / | #59: Chemical | ChemComp-SF4 / |
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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: Respirasome / Type: COMPLEX / Details: supercomplex of complex I, III and IV / Entity ID: #1-#51 / Source: NATURAL |
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Molecular weight | Value: 1.7 MDa / Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.7 |
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: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K / Details: 10 s blotting |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 57797 X / Nominal defocus max: 4300 nm / Nominal defocus min: 1300 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 4300 nm / Cs: 2.2 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: OTHER / Num. of real images: 3592 / Details: Falcon III |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 46 / Used frames/image: 2-46 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Particle selection | Num. of particles selected: 156519 / Details: particles were selected manually | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17093 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |