+Open data
-Basic information
Entry | Database: PDB / ID: 7tlj | ||||||
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Title | Rhodobacter sphaeroides Mitochondrial respiratory chain complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer | ||||||
Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / intracellular membrane-bounded organelle / heme binding ...respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / intracellular membrane-bounded organelle / heme binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Cereibacter sphaeroides (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
Authors | Xia, D. / Zhou, F. / Esser, L. / Huang, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin Authors: Xia, D. / Esser, L. / Zhou, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tlj.cif.gz | 821.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tlj.ent.gz | 554.3 KB | Display | PDB format |
PDBx/mmJSON format | 7tlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/7tlj ftp://data.pdbj.org/pub/pdb/validation_reports/tl/7tlj | HTTPS FTP |
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-Related structure data
Related structure data | 25989MC 7tayC 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
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 50087.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q02761 #2: Protein | Mass: 29589.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cyt c1 with c-terminal hexa his tag / Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petC, fbcC / Production host: Escherichia coli (E. coli) / References: UniProt: Q02760 #3: Protein | Mass: 19928.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase #4: Protein | Mass: 14415.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost ...Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost during crystallization. Here in our CryoEM structure we see it for the first time - even though only one helix Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P16536 |
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-Non-polymers , 5 types, 12 molecules
#5: Chemical | ChemComp-HEM / #6: Chemical | #7: Chemical | #8: Chemical | #9: 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 of rhodobacter sphaeroides inhibited by pyramoxadone Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 250 kDa/nm / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Cereibacter sphaeroides (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Cytochrome bc1 complex from Rhodobacter sphaeroides with inhibitor pyramoxadone (PQ4), frozen stock 84 mg/ml. dilute to 8 mg/ml in buffer 50mM TrisHCl, pH7.5/0.16% SMC/0.01% GDN/1mM EDTA | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K Details: 3 ul of sample blot for 3 sec. blot force 20. glow discharge for 60 sec with easy glow |
-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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 60241 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 836 nm / Calibrated defocus max: 3434 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): 80 K / Temperature (min): 80 K |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 20306 / Details: 0.05s per frame for total 50 frames. |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 4092 / Height: 5760 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5498641 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 725256 / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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