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Yorodumi- PDB-8qc1: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qc1 | |||||||||
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Title | Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement) | |||||||||
Components | (NADH dehydrogenase subunit ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs | |||||||||
Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane Similarity search - Function | |||||||||
Biological species | Paracoccus denitrificans PD1222 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Ivanov, B.S. / Bridges, H.R. / Hirst, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Respiratory complex I from Paracoccus denitrificans Authors: Ivanov, B.S. / Bridges, H.R. / Hirst, J. / Jarman, O.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qc1.cif.gz | 250.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qc1.ent.gz | 193.9 KB | Display | PDB format |
PDBx/mmJSON format | 8qc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qc1_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8qc1_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8qc1_validation.xml.gz | 63 KB | Display | |
Data in CIF | 8qc1_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qc1 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qc1 | HTTPS FTP |
-Related structure data
Related structure data | 18325MC 8qbyC C: citing same article (ref.) M: map data used to model this data |
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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
-NADH dehydrogenase subunit ... , 2 types, 2 molecules ML
#1: Protein | Mass: 56519.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B480, NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 77811.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B481, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 6 types, 130 molecules
#3: Chemical | ChemComp-3PH / #4: Chemical | ChemComp-3PE / #5: Chemical | ChemComp-CDL / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-P5S / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Paracoccus denitrificans PD1222 (bacteria) |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.4 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 16814 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146603 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | Details: Model Angelo / Source name: Other / Type: in silico model |