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Yorodumi- PDB-8qt7: Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qt7 | ||||||
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Title | Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase in complex with NADPH | ||||||
Components | FAD-binding FR-type domain-containing protein | ||||||
Keywords | MEMBRANE PROTEIN / NADPH oxidase / ROS producing / flavoprotein / heme protein | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / membrane Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Dubach, V.R.A. / San Segundo-Acosta, P. / Murphy, B.J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qt7.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qt7.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qt7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8qt7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8qt7_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 8qt7_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/8qt7 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/8qt7 | HTTPS FTP |
-Related structure data
Related structure data | 18645MC 8qt6C 8qt9C 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
#1: Protein | Mass: 46060.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: spr0531 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q8CZ28 | ||||
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#2: Chemical | ChemComp-NDP / | ||||
#3: Chemical | ChemComp-FAD / | ||||
#4: Chemical | #5: 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 |
-Sample preparation
Component | Name: Streptococcus pneumoniae NADPH oxidase with FAD and heme cofactors Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.046 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Streptococcus pneumoniae (bacteria) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41 | ||||||||||||||||||||||||||||||
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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: 22259 / 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 |
-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: 14458708 Details: These are the combined particles from two different Topaz models and a crYOLO model and contains duplicate particles. | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 591137 / Algorithm: FOURIER SPACE Details: Final refinement was local refinement in cryoSPARC 4.0 with a mask excluding the detergent micelle. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: Initial model was fit using ChimeraX and refined with Coot and PHENIX. | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: Initial model was the previously made SpNOX model without substrate bound Source name: Other / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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