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- PDB-9r8w: Cryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in comple... -

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Basic information

Entry
Database: PDB / ID: 9r8w
TitleCryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in complex with weakly bound effector CCG28 (C2-symmetry)
Components
  • Disease resistance protein ADR2
  • Effector CCG28
KeywordsPLANT PROTEIN / TIR NLR / Resistosome / Oomycete / effector WRR4A
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 / 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: Biorxiv / Year: 2026
Title: Structural basis for the broad recognition specificity of an Arabidopsis immune receptor
Authors: Zhao, H. / Szymansky, C.M. / Lyu, X. / Huang, J. / Derbyshire, P. / Menke, F.L.H. / Webster, M.W. / Kamoun, S. / Selvaraj, M. / Jones, J.D.G.
History
DepositionMay 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 13, 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
Q: Effector CCG28
R: Effector CCG28
S: Effector CCG28
A: Disease resistance protein ADR2
B: Disease resistance protein ADR2
C: Disease resistance protein ADR2
D: Disease resistance protein ADR2
P: Effector CCG28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)703,07112
Polymers701,3638
Non-polymers1,7094
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
Effector CCG28


Mass: 61221.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Albugo candida (eukaryote) / Production host: Nicotiana benthamiana (plant)
#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
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: WRR4A tetramer in complex with loosely bound effector CCG28
Type: COMPLEX / 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: 150mM NaCl, 150mM Tris HCl,
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 5 K

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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: 27000 nm / Nominal defocus min: 14000 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 recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFINDCTF correction
7Cootmodel fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98507 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: FLEXIBLE FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00434043
ELECTRON MICROSCOPYf_angle_d0.64446057
ELECTRON MICROSCOPYf_dihedral_angle_d7.7514586
ELECTRON MICROSCOPYf_chiral_restr0.0445286
ELECTRON MICROSCOPYf_plane_restr0.0045831

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