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- PDB-8bgw: CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bgw | |||||||||
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Title | CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution | |||||||||
![]() | Nitric oxide reductase subunit B | |||||||||
![]() | MEMBRANE PROTEIN / quinol-dependent Nitric Oxide Reductase / proton transfer / quinol binding / ubiquinol oxidase | |||||||||
Function / homology | ![]() nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / cytochrome-c oxidase activity / aerobic respiration / heme binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
![]() | Flynn, A. / Antonyuk, S.V. / Eady, R.R. / Muench, S.P. / Hasnain, S.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Authors: Alex J Flynn / Svetlana V Antonyuk / Robert R Eady / Stephen P Muench / S Samar Hasnain / ![]() Abstract: Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where ...Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo, a respiratory quinol oxidase. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332 KB | Display | ![]() |
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PDB format | ![]() | 265.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 16041MC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/10M.gif)
![](data/chem/img/10M.gif)
#1: Protein | Mass: 84724.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0D6H8R3, nitric oxide reductase (cytochrome c) #5: Sugar | |
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-Non-polymers , 6 types, 472 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/LOP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/LOP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | #4: Chemical | #6: Chemical | #7: Chemical | ChemComp-LOP / ( #8: Water | ChemComp-HOH / | |
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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: quinol-dependent Nitric Oxide Reductase / Type: CELL / Details: quinol-dependent Nitric Oxide Reductase / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.84651 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 / Details: 50mM Tris-HCl, 150mM NaCl, 0.05% DTM |
Buffer component | Conc.: 50 mM / Name: Tris-HCL / Formula: Tris-HCL |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Sample at 3 mg/mL was applied to glow-discharged Quantifoil Au R1.2/1.3 holey carbo grids |
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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: 130000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 114 K / Temperature (min): 80 K |
Image recording | Average exposure time: 6.11 sec. / Electron dose: 34.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5466 |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 10 eV |
Image scans | Width: 4096 / Height: 4096 |
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Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3000000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 404950 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 47 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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