+Open data
-Basic information
Entry | Database: PDB / ID: 6fo2 | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of bovine cytochrome bc1 with no ligand bound | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / Cryo-EM / Inhibitor binding / cytochrome bc1 | ||||||
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 / oxidoreductase activity / mitochondrial inner membrane / 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: 4.4 Å | ||||||
Authors | Johnson, R.M. / Amporndanai, K. / O'Neill, P.M. / Fishwick, C.W.G. / Jamson, A.H. / Rawson, S.D. / Hasnain, S.S. / Antonyuk, S.V. / Muench, S.P. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: IUCrJ / Year: 2018 Title: X-ray and cryo-EM structures of inhibitor-bound cytochrome complexes for structure-based drug discovery. Authors: Kangsa Amporndanai / Rachel M Johnson / Paul M O'Neill / Colin W G Fishwick / Alexander H Jamson / Shaun Rawson / Stephen P Muench / S Samar Hasnain / Svetlana V Antonyuk / Abstract: Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. ...Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome that may be available from parasites, all efforts have been focused on homologous cytochrome complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6fo2.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fo2.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6fo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fo2_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fo2_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6fo2_validation.xml.gz | 106.2 KB | Display | |
Data in CIF | 6fo2_validation.cif.gz | 161.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/6fo2 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/6fo2 | HTTPS FTP |
-Related structure data
Related structure data | 4288MC 4286C 4292C 5okdC 6fo0C 6fo6C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Cytochrome b-c1 complex subunit ... , 8 types, 16 molecules NAOBRESFTGUHVIWJ
#1: Protein | Mass: 52796.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800 #2: Protein | Mass: 48204.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004 #5: Protein | Mass: 29586.842 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: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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: 10638.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126 #9: Protein/peptide | Mass: 1652.936 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: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130 |
---|
-Protein , 2 types, 4 molecules PCQD
#3: Protein | Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157 #4: Protein | Mass: 35343.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125 |
---|
-Non-polymers , 2 types, 6 molecules
#11: Chemical | ChemComp-HEM / #12: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Bovine cytochrome bc1 in the absence of any inhibitor. Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.48 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) / Cellular location: Mitochondria / Organ: Heart | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot for 6 seconds with a blot force of 6 before plunge-freezing |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal magnification: 79000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12 sec. / Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3256 |
Image scans | Movie frames/image: 20 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 260201 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57571 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|