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Open data
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Basic information
Entry | Database: PDB / ID: 8evu | ||||||
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Title | Cryo EM structure of Vibrio cholerae NQR | ||||||
![]() | (Na(+)-translocating NADH-quinone reductase subunit ...) x 6 | ||||||
![]() | ELECTRON TRANSPORT / TRANSLOCASE / complex | ||||||
Function / homology | ![]() NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity ...NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5804 Å | ||||||
![]() | Fuller, J.R. / Juarez, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel cofactor binding motifs, electron transfer and ion pumping mechanisms of the respiratory complex NQR Authors: Juarez, O. / Fuller, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 377.8 KB | Display | ![]() |
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PDB format | ![]() | 244.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28637MC ![]() 8ew3C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Na(+)-translocating NADH-quinone reductase subunit ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 48680.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9KPS1, NADH:ubiquinone reductase (Na+-transporting) |
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#2: Protein | Mass: 45390.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9KPS2, NADH:ubiquinone reductase (Na+-transporting) |
#3: Protein | Mass: 27652.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0C6E0, NADH:ubiquinone reductase (Na+-transporting) |
#4: Protein | Mass: 22853.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9X4Q6, NADH:ubiquinone reductase (Na+-transporting) |
#5: Protein | Mass: 21481.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9X4Q7, NADH:ubiquinone reductase (Na+-transporting) |
#6: Protein | Mass: 45113.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9X4Q8, NADH:ubiquinone reductase (Na+-transporting) |
-Non-polymers , 4 types, 5 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/FES.gif)
#7: Chemical | #8: Chemical | ChemComp-RBF / | #9: Chemical | ChemComp-UQ1 / | #10: Chemical | ChemComp-FES / | |
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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 |
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Sample preparation
Component | Name: Na(+)-translocating NADH-quinone reductase / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 7 / Details: 100 mM KCl, 1 mM EDTA, 50 mM HEPES, pH 7.0 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: Gatan Solarus plasma cleaner operated at 20W and using ambient/room air Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: A 3.5 uL droplet of sample was applied to the grid surface and blotted for 4 s before plunging into liquid ethane. |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.66 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3159 / Details: 50 e-/A2 fractionated over 40 movie frames |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
Software |
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EM software |
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Image processing | Details: Micrograph movies were summed and dose-weighted using the motion correction algorithm implemented in RELION. | ||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 304335 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5804 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106466 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation Details: The model was refined by iterating between manual edits in Coot, molecular dynamics-guided edits using the ISOLDE ChimeraX package, and automated real-space refinement in Phenix. Models that ...Details: The model was refined by iterating between manual edits in Coot, molecular dynamics-guided edits using the ISOLDE ChimeraX package, and automated real-space refinement in Phenix. Models that had been automatically rebuilt using Rosetta were used as guides during manual refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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