+Open data
-Basic information
Entry | Database: PDB / ID: 8xuo | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of tomato NRC2 dimer | ||||||
Components | NRC2 | ||||||
Keywords | PLANT PROTEIN / tomato / helper NLR / dimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||
Authors | Sun, Y. / Ma, S.C. / Chai, J.J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of tomato NRC2 dimer Authors: Ma, S.C. / Chai, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xuo.cif.gz | 306.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xuo.ent.gz | 246.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/8xuo ftp://data.pdbj.org/pub/pdb/validation_reports/xu/8xuo | HTTPS FTP |
---|
-Related structure data
Related structure data | 38679MC 8xuqC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 86267.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence reference for NRC2 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q7IF17. Regarding SlNRC2 with the accession number ...Details: Sequence reference for NRC2 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q7IF17. Regarding SlNRC2 with the accession number Solyc10g047320 in the SGN database, here is the link: https://solgenomics.net/locus/36701/view. The source article for SlNRC2 is "Helper NLR proteins NRC2a/b and NRC3 but not NRC1 are required for Pto-mediated cell death and resistance in Nicotiana benthamiana" by Wu, Chih-Hang et al. The article was published in The New Phytologist, volume 209, issue 4, in 2016. The DOI is 10.1111/nph.13764. Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: 101243750 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A3Q7IF17 #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NRC2 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Solanum lycopersicum (tomato) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
---|---|
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 560935 / Symmetry type: POINT |