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- PDB-9jbn: Cryo-EM structure of the Arabidopsis EDS1-PAD4-ADR1 immune comple... -

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Basic information

Entry
Database: PDB / ID: 9jbn
TitleCryo-EM structure of the Arabidopsis EDS1-PAD4-ADR1 immune complex in the presence of pRib-AMP
Components
  • PAD4
  • Probable disease resistance protein At5g04720
  • Protein EDS1
KeywordsIMMUNE SYSTEM / TIR signaling / EDS1 / PAD4 / ADR1 / pRib-AMP / cryo-EM
Function / homology
Function and homology information


aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast ...aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast / defense response / ADP binding / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / cell surface receptor signaling pathway / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Arabidopsis broad-spectrum mildew resistance protein RPW8 / Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Adaptor protein Cbl, N-terminal domain superfamily / Apoptotic protease-activating factors, helical domain ...Arabidopsis broad-spectrum mildew resistance protein RPW8 / Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Adaptor protein Cbl, N-terminal domain superfamily / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Lipases, serine active site. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 5-O-phosphono-beta-D-ribofuranose / PAD4 / Probable disease resistance protein At5g04720 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang, H. / Tan, J. / Cui, X. / Song, S. / Yan, C. / Qi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Switch of TIR signaling by a Ca2+ sensor activates ADR1 recognition of pRib-AMP-bound EDS1-PAD4 for stomatal immunity
Authors: Wang, H. / Tan, J. / Cui, X. / Song, S. / Yan, C. / Qi, T.
History
DepositionAug 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data 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
A: Protein EDS1
B: PAD4
C: Probable disease resistance protein At5g04720
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,0795
Polymers224,5023
Non-polymers5772
Water4,936274
1


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

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Protein EDS1 / Enhanced disease susceptibility 1


Mass: 71784.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q9SU72
#2: Protein PAD4


Mass: 61054.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At3g46840, AN1_LOCUS15608 / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A178V847
#3: Protein Probable disease resistance protein At5g04720


Mass: 91662.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g04720, MUK11.4, T1E3.80 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q9LZ25

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 275 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: EDS1-PAD4-ADR1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Nicotiana benthamiana (plant)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1779204 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412844
ELECTRON MICROSCOPYf_angle_d0.56117384
ELECTRON MICROSCOPYf_dihedral_angle_d5.0671726
ELECTRON MICROSCOPYf_chiral_restr0.0411937
ELECTRON MICROSCOPYf_plane_restr0.0052219

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