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- PDB-9qww: Cryo-EM structure of plant resistance protein NRC2 dimer bound to... -

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Basic information

Entry
Database: PDB / ID: 9qww
TitleCryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15
Components
  • NRC2a
  • Truncated secreted SPRY domain-containing protein 15
KeywordsPLANT PROTEIN / Helper resistance protein / Plant immunity / Suppressor
Function / homology
Function and homology information


defense response to other organism / ADP binding / defense response to virus / ATP binding
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / : / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / : / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / : / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / : / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Truncated secreted SPRY domain-containing protein 15 / NRC2a
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
Globodera rostochiensis (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSelvaraj, M. / Kamoun, S. / Contreras, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Gatsby Charitable Foundation United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15 (SS15)
Authors: Selvaraj, M. / Kamoun, S. / Contreras, M.
History
DepositionApr 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NRC2a
B: Truncated secreted SPRY domain-containing protein 15
D: Truncated secreted SPRY domain-containing protein 15
C: NRC2a


Theoretical massNumber of molelcules
Total (without water)253,3444
Polymers253,3444
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NRC2a


Mass: 101270.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana benthamiana (plant) / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A0S3ANR1
#2: Protein Truncated secreted SPRY domain-containing protein 15


Mass: 25402.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Globodera rostochiensis (invertebrata) / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A024E1S8
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Dimer of NRC2 bound with SS15 effector / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Nicotiana benthamiana (plant)
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.5
Details: 150mM NaCl, 50mM Tris HCl (pH 7.5), 5mM DTT, 5% glycerol,
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.3mg/ml
Specimen supportGrid material: COPPER / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 27000 nm / Nominal defocus min: 14000 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 70 K
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5174
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV / Phase plate: OTHER

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2044827
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102500 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314706
ELECTRON MICROSCOPYf_angle_d0.74819885
ELECTRON MICROSCOPYf_dihedral_angle_d8.7672003
ELECTRON MICROSCOPYf_chiral_restr0.0482219
ELECTRON MICROSCOPYf_plane_restr0.0062550

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