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- EMDB-53235: Cryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-53235
TitleCryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in complex with effector CCG40
Map dataThis is postprocessed final map in C4 symmetry
Sample
  • Complex: Activated WRR4A resistosome in complex with CCG40 effector
    • Protein or peptide: CCG40
    • Protein or peptide: Disease resistance protein ADR2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsTIR NLR / Arabidopsis / Resistosome / Effector / Oomycete / PLANT PROTEIN
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
CCG40 / Disease resistance protein ADR2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Albugo candida (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhao H / Lukoyanova N / Selvaraj M / Jones J
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53235.png

Downloads & links

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Map

FileDownload / File: emd_53235.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is postprocessed final map in C4 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.0684298 - 0.116119616
Average (Standard dev.)0.00022510803 (±0.002503098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53235_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: This is the same postprocessed map that was...

Fileemd_53235_additional_1.map
AnnotationThis is the same postprocessed map that was enhanced in interpretation by EMREADY
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: This is unsharpened, refine3D map from relion

Fileemd_53235_additional_2.map
AnnotationThis is unsharpened, refine3D map from relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is halfmap 2

Fileemd_53235_half_map_1.map
AnnotationThis is halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: this is halfmap1

Fileemd_53235_half_map_2.map
Annotationthis is halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Activated WRR4A resistosome in complex with CCG40 effector

EntireName: Activated WRR4A resistosome in complex with CCG40 effector
Components
  • Complex: Activated WRR4A resistosome in complex with CCG40 effector
    • Protein or peptide: CCG40
    • Protein or peptide: Disease resistance protein ADR2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Activated WRR4A resistosome in complex with CCG40 effector

SupramoleculeName: Activated WRR4A resistosome in complex with CCG40 effector
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: This contains NB-ARC domain and LRR domain of WRR4A and CCG40 effector
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: CCG40

MacromoleculeName: CCG40 / type: protein_or_peptide / ID: 1
Details: This is CCG40 effector from Albugo candida oomycete.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Albugo candida (eukaryote)
Molecular weightTheoretical: 24.496584 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MAYRLFLTLW VYQIYHVVGV LKSGELRIKK TDSRNSLSLC QACVLNKLGA SRMKLINDDE EVATYKITGS DFVFANLKVD CSGVNECNI DKIIPLSWPS MMPNEIALSA RSPQLYVSAS ESSSSVLCMD CLQENAAARF ISKFRVNKLK VVRIVYMIYG A LLNTQHLK ...String:
MAYRLFLTLW VYQIYHVVGV LKSGELRIKK TDSRNSLSLC QACVLNKLGA SRMKLINDDE EVATYKITGS DFVFANLKVD CSGVNECNI DKIIPLSWPS MMPNEIALSA RSPQLYVSAS ESSSSVLCMD CLQENAAARF ISKFRVNKLK VVRIVYMIYG A LLNTQHLK CTDYCPGLTI LEEMDNSKQL VQIFRSEEHL PLSRIRHHVI QCNALSHK

UniProtKB: CCG40

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Macromolecule #2: Disease resistance protein ADR2

MacromoleculeName: Disease resistance protein ADR2 / type: protein_or_peptide / ID: 2
Details: This is activated plant immune receptor WRR4A assembled as a resistosome with effector bound to it.
Number of copies: 4 / Enantiomer: LEVO / EC number: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 114.119039 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MASSSSSPRN WRYNVFTSFH GPDVRIKFLS HLRQQFVYNG ITMFDDNGIE RSQIIAPALK KAIGESRVAI VLLSKNYASS SWCLDELLE ILKCKEYIGQ IVMTVFYEVD PSHVRKQTGD FGIAFKETCA HKTEEERSKW SQALTYVGNI AGEDFIHWKD E AKMIEKIA ...String:
MASSSSSPRN WRYNVFTSFH GPDVRIKFLS HLRQQFVYNG ITMFDDNGIE RSQIIAPALK KAIGESRVAI VLLSKNYASS SWCLDELLE ILKCKEYIGQ IVMTVFYEVD PSHVRKQTGD FGIAFKETCA HKTEEERSKW SQALTYVGNI AGEDFIHWKD E AKMIEKIA RDVSTKINVT PCRDFDDMVG LERHLKEMVS LLDLDKEGVK MVGISGPAGI GKSTIAKALH SRHSSTFQHN CF VDNLWEN YKICTGEHGV KLRLHEQFVS KILKQNGLEL THLSVIKDRL QDKKVLIILD DVESLAQLET LADMTWFGPG SRV IVTTEN KEILQQHGIG DIYQVGYPSE SEALTIFCLS AFKQASPPDG FMDLADEVVR ICDKLPLALC VLGSSLLRKS QTDW EDELP RLRNCLDGIE SVLKVGFESL NEKDQALFLY ITVFFNYECA DHVTLMLAKS NLNVRLGLKN LANRYLIHID HDQKK RVVV HRLLRVMAIQ VCTKQKPWKS QILVDAEKIA YVLEEATGNR SIKGVSFDTA EIDELMISPK AFEKMCNLLF LKVYDA GWH TGKRKLDIPE DIKFPRTIRL FHWDAYSGKR LPSSFFAENL VEVNMQDSEL QKLWEGTQCL ANLKKIDLSR SSCLTEL PD LSNATNLEDL YVGSCTALVE LPSSIGNLHK LAHIMMYSCE SLEVIPSLIN LTSLTFLNMN KCSRLRRFPD IPTSIEDV Q VTGTTLEELP ASLTHCSGLQ TIKISGSVNL KIFYTELPVS VSHINISNSG IEWITEDCIK GLHNLHDLCL SGCKRLVSL PELPRSLKIL QADDCDSLES LNGHLNTPNA ELYFANCFKL DAEARRAIIQ QSFVSGWALL PGLEVPPEFG HRARGNSLII PYSASNRFK VCVVMSLNHH QPFELVPRNL LYRWTVIGDS VSSDEKTFHL SHMFNADSVN SKLQKPHLFI FHSCLPFIFH S CLPFIFDI SNIMLEFSSE YKDFDILECG VQILTDETDE RNIWGSLVF

UniProtKB: Disease resistance protein ADR2

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Details: 150 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: GRAPHENE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 4 K / Instrument: LEICA EM GP
Details: The sample was applied on copper EM grid, with graphene oxide backing..
Detailsthis is flag tag purified protein used for EM grid preparation at a concentration of 0.2mg/ml

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8009 / Average exposure time: 1.9 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 520094
CTF correctionSoftware - Name: RELION / Details: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: This is an abinitio starting model created from a set of particles using Relion 3D Initial reference module
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 117347
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3
Details: A 3D classification with 4 classes were performed on final set of particles selected after several rounds of 2D-classification
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsFitting in the final map using COOT and Chimera.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qlv:
Cryo-EM structure of Arabidopsis TIR-NLR WRR4A tetramer in complex with effector CCG40

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