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Yorodumi- PDB-8qby: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qby | |||||||||
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Title | Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs | |||||||||
Function / homology | Function and homology information NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity ...NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / electron transport chain / protein modification process / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / methylation / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Paracoccus denitrificans PD1222 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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 | 8qby.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qby.ent.gz | 857.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qby_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 8qby_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8qby_validation.xml.gz | 159.3 KB | Display | |
Data in CIF | 8qby_validation.cif.gz | 241.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/8qby ftp://data.pdbj.org/pub/pdb/validation_reports/qb/8qby | HTTPS FTP |
-Related structure data
Related structure data | 18324MC 8qc1C 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
-NADH-quinone ... , 11 types, 11 molecules KGINHFDAJCB
#1: Protein | Mass: 10863.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B482, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#2: Protein | Mass: 73289.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B489, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#4: Protein | Mass: 18925.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B486 |
#6: Protein | Mass: 52564.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B479 |
#7: Protein | Mass: 38861.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B487 |
#8: Protein | Mass: 47281.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B491 |
#9: Protein | Mass: 46811.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B495 |
#11: Protein | Mass: 13686.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B498 |
#12: Protein | Mass: 21835.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: P29922 |
#15: Protein | Mass: 23920.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B496 |
#16: Protein | Mass: 19525.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B497 |
-Protein , 4 types, 4 molecules tqRQ
#3: Protein | Mass: 23528.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B5L6 |
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#10: Protein | Mass: 14432.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B1H8 |
#13: Protein | Mass: 7069.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B357 |
#14: Protein | Mass: 12048.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B1M0 |
-NADH dehydrogenase subunit ... , 3 types, 3 molecules ELM
#5: Protein | Mass: 26145.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Paracoccus denitrificans PD1222 (bacteria) References: UniProt: A1B494 |
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#17: 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 |
#18: 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 |
-Non-polymers , 13 types, 1129 molecules
#19: Chemical | ChemComp-SF4 / #20: Chemical | #21: Chemical | ChemComp-NA / | #22: Chemical | ChemComp-3PH / #23: Chemical | #24: Chemical | ChemComp-CA / #25: Chemical | ChemComp-3PE / #26: Chemical | #27: Chemical | ChemComp-FMN / | #28: Chemical | #29: Chemical | ChemComp-ZN / | #30: Chemical | ChemComp-U10 / | #31: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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-#18 / 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 |
Specimen support | Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for ...Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for two days under anaerobic conditions. The grids were then washed in 100% ethanol and dried three times prior to sample application. Grid material: GOLD / Grid type: UltrAuFoil R0./1 |
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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146603 / Algorithm: BACK PROJECTION / 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 |