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- PDB-9qlv: Cryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in comple... -

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Basic information

Entry
Database: PDB / ID: 9qlv
TitleCryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in complex with effector CCG40
Components
  • CCG40
  • Disease resistance protein ADR2
KeywordsPLANT PROTEIN / TIR NLR / Arabidopsis / Resistosome / Effector / Oomycete
Function / homology
Function and homology information


defense response to oomycetes / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / defense response to fungus / defense response / ADP binding / cellular response to UV / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / : / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance ...Leucine-rich repeat 3 / Leucine Rich Repeat / : / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CCG40 / Disease resistance protein ADR2
Similarity search - Component
Biological speciesAlbugo candida (eukaryote)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhao, H. / Lukoyanova, N. / Selvaraj, M. / Jones, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Gatsby Charitable Foundation United Kingdom
CitationJournal: To Be Published
Title: Structural basis for the broad recognition and activation of an Arabidopsis immune receptor
Authors: Zhao, H. / Lukoyanova, N. / Selvaraj, M. / Jones, J.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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

Downloads & links

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Assembly

Deposited unit
P: CCG40
Q: CCG40
R: CCG40
S: CCG40
A: Disease resistance protein ADR2
B: Disease resistance protein ADR2
C: Disease resistance protein ADR2
D: Disease resistance protein ADR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,17112
Polymers554,4628
Non-polymers1,7094
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, This is a protein complex of about 600kDa size in total.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
CCG40


Mass: 24496.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This is CCG40 effector from Albugo candida oomycete.
Source: (gene. exp.) Albugo candida (eukaryote) / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A8F4TCV5
#2: Protein
Disease resistance protein ADR2 / Protein ACTIVATED DISEASE RESISTANCE 2 / Protein WHITE RUST RESISTANCE 4


Mass: 114119.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This is activated plant immune receptor WRR4A assembled as a resistosome with effector bound to it.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADR2, WRR4, At1g56510, F13N6.5 / Production host: Nicotiana benthamiana (plant)
References: UniProt: Q9C7X0, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
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: Activated WRR4A resistosome in complex with CCG40 effector
Type: COMPLEX
Details: This contains NB-ARC domain and LRR domain of WRR4A and CCG40 effector
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.5
Details: 150 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM MgCl2
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: this is flag tag purified protein used for EM grid preparation at a concentration of 0.2mg/ml
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 4 K
Details: The sample was applied on copper EM grid, with graphene oxide backing.

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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: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.9 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8009

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2EPU3.4image acquisition
4RELIONCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION53D reconstruction
13PHENIXmodel refinement
CTF correctionDetails: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 520094
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117347 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Fitting in the final map using COOT and Chimera.
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328288
ELECTRON MICROSCOPYf_angle_d0.69738288
ELECTRON MICROSCOPYf_dihedral_angle_d8.4313788
ELECTRON MICROSCOPYf_chiral_restr0.0464428
ELECTRON MICROSCOPYf_plane_restr0.0044860

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