+Open data
-Basic information
Entry | Database: PDB / ID: 9fp6 | ||||||||||||||||||||||||
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Title | Structure of the NbNRC2 hexameric resistosome | ||||||||||||||||||||||||
Components | NRC2a | ||||||||||||||||||||||||
Keywords | IMMUNE SYSTEM / Plant immunity / complex | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Nicotiana benthamiana (plant) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||
Authors | Webster, M.W. / Madhuprakash, J. / Kamoun, S. | ||||||||||||||||||||||||
Funding support | United Kingdom, European Union, 7items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the NbNRC2 hexameric resistosome Authors: Webster, M.W. / Madhuprakash, J. / Kamoun, S. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fp6.cif.gz | 869.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fp6.ent.gz | 708 KB | Display | PDB format |
PDBx/mmJSON format | 9fp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fp6_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 9fp6_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 9fp6_validation.xml.gz | 126 KB | Display | |
Data in CIF | 9fp6_validation.cif.gz | 187.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/9fp6 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/9fp6 | HTTPS FTP |
-Related structure data
Related structure data | 50637MC 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: 101270.000 Da / Num. of mol.: 6 / Mutation: L9E, L13E, L17E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana benthamiana (plant) / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A0S3ANR1 #2: Chemical | ChemComp-ATP / Has ligand of interest | N | |
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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 |
-Sample preparation
Component | Name: NbNRC2a / Type: COMPLEX Details: The NbNRC2 was activated in planta to a hexameric resistosome using the sensor Rx and PVX coat protein. Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.606 MDa / Experimental value: YES |
Source (natural) | Organism: Nicotiana benthamiana (plant) |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) |
Buffer solution | pH: 7.5 Details: 100mM Tris HCl (pH 7.5), 150 mM NaCl, 1 mM MgCl2, 3% glycerol |
Specimen | Conc.: 2.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 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: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.95 sec. / Electron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12908 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 391586 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205897 / Algorithm: BACK PROJECTION / Symmetry type: POINT |