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- PDB-8xuv: Cryo-EM structure of tomato NRC2 filament -

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Basic information

Entry
Database: PDB / ID: 8xuv
TitleCryo-EM structure of tomato NRC2 filament
ComponentsNRC2
KeywordsPLANT PROTEIN / tomato / helper NLR / dimer
Function / homology
Function and homology information


defense response to other organism / ADP binding
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / NRC1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSun, Y. / Ma, S.C. / Chai, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of tomato NRC2 filament
Authors: Ma, S.C. / Chai, J.J.
History
DepositionJan 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NRC2
B: NRC2
C: NRC2
D: NRC2
E: NRC2
F: NRC2
G: NRC2
H: NRC2
I: NRC2
J: NRC2
K: NRC2
L: NRC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,229,03236
Polymers1,215,98512
Non-polymers13,04724
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
NRC2


Mass: 101332.078 Da / Num. of mol.: 12
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
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: NRC2 filament / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Solanum lycopersicum (tomato)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -55.85 ° / Axial rise/subunit: 64.04 Å / Axial symmetry: C3
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280426 / Symmetry type: HELICAL

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