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Open data
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Basic information
Entry | Database: PDB / ID: 8qt6 | ||||||
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Title | Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase | ||||||
![]() | FAD-binding FR-type domain-containing protein | ||||||
![]() | MEMBRANE PROTEIN / NADPH oxidase / ROS producing / flavoprotein / heme protein | ||||||
Function / homology | ![]() 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å | ||||||
![]() | Dubach, V.R.A. / San Segundo-Acosta, P. / Murphy, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mechanistic insight into Streptococcus pneumoniae NADPH oxidase Authors: Dubach, V.R.A. / San Segundo-Acosta, P. / Murphy, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.6 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18644MC ![]() 8qt7C ![]() 8qt9C 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
#1: Protein | Mass: 46060.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 700 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 |
Image recording | Average exposure time: 3.96 sec. / Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18433 / Details: Movies were collected in EER format. |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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Image processing | Details: Movies were collected in EER format and not gain corrected | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8765912 Details: These are the combined particles from two different Topaz models and a crYOLO model and contains duplicate particles. | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397972 / Algorithm: FOURIER SPACE Details: Final refinement was local refinement in cryoSPARC 4.0 using a mask that excludes the detergent micelle. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: Q8CZ28 / Chain residue range: 1-400 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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