+Open data
-Basic information
Entry | Database: PDB / ID: 8p65 | |||||||||
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Title | Cytochrome bc1 complex (Bos taurus) | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Electron Transport Chain / Complex III / Respiratory Complex | |||||||||
Function / homology | Function and homology information Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Phillips, B.P. / Barra, I.M.C.C. / Meier, T.K. / Rimle, L. / von Ballmoos, C. | |||||||||
Funding support | Switzerland, United Kingdom, 2items
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Citation | Journal: To Be Published Title: Cytochrome bc1 complex (Bos taurus) Authors: Phillips, B.P. / Barra, I.M.C.C. / Meier, T.K. / Rimle, L. / von Ballmoos, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p65.cif.gz | 828.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p65.ent.gz | 677.5 KB | Display | PDB format |
PDBx/mmJSON format | 8p65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p65_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8p65_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8p65_validation.xml.gz | 122.9 KB | Display | |
Data in CIF | 8p65_validation.cif.gz | 185.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/8p65 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p65 | HTTPS FTP |
-Related structure data
Related structure data | 17461MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules ANBOERFSGTHUIVJWKX
#1: Protein | Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P31800 #2: Protein | Mass: 46576.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / 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) / Tissue: Heart / References: UniProt: P13272, quinol-cytochrome-c reductase #6: Protein | Mass: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P00129 #7: Protein | Mass: 9737.223 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: 5497.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272 #10: Protein | Mass: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P00130 #11: Protein/peptide | Mass: 5705.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P07552 |
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-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P00157 #4: Protein | Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Heart / References: UniProt: P00125, quinol-cytochrome-c reductase |
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-Non-polymers , 3 types, 8 molecules
#12: Chemical | ChemComp-HEM / #13: Chemical | #14: Chemical | |
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-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 |
-Sample preparation
Component | Name: Cytochrome bc1 complex (bos taurus) / Type: COMPLEX Details: Cytochrome bc1 complex purified natively from bovine heart tissue Entity ID: #1-#11 / Source: NATURAL |
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Molecular weight | Value: 0.486 MDa / Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Monodisperse sample was purified un-tagged from bovine heart tissue and reconstituted into peptidiscs before freezing. |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Blot time of 4s with blot force of -3 |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 85000 X / Calibrated magnification: 85000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2750 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90.5 K / Temperature (min): 80 K / Residual tilt: 10 mradians |
Image recording | Average exposure time: 8 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3947 |
EM imaging optics | Energyfilter name: TFS Selectris / Details: Tuned using TFS Sherpa Software / Energyfilter slit width: 10 eV / Phase plate: OTHER |
Image scans | Sampling size: 1.416 µm / Width: 4000 / Height: 4000 |
-Processing
EM software |
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CTF correction | Details: CryoSPARC's own CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 154469 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140138 / Algorithm: FOURIER SPACE / Details: FSC calculated in PDB server. / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 96.9 / Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6FO2 Accession code: 6FO2 / Source name: PDB / Type: experimental model |