9JBN | pdb_00009jbn

Cryo-EM structure of the Arabidopsis EDS1-PAD4-ADR1 immune complex in the presence of pRib-AMP

• PDB DOI: https://doi.org/10.2210/pdb9JBN/pdb
• EM Map EMD-61320: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Arabidopsis thaliana
• Expression System: Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2024-08-27 Released: 2025-09-03 
• Deposition Author(s): Wang, H., Tan, J., Cui, X., Song, S., Yan, C., Qi, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Switch of TIR signaling by a Ca2+ sensor activates ADR1 recognition of pRib-AMP-bound EDS1-PAD4 for stomatal immunity

Wang, H., Tan, J., Cui, X., Song, S., Yan, C., Qi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 225.08 kDa 
• Atom Count: 12,842 
• Modeled Residue Count: 1,561 
• Deposited Residue Count: 1,975 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein EDS1	A	623	Arabidopsis thaliana	Mutation(s): 0  Gene Names: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40
UniProt
Find proteins for Q9SU72 (Arabidopsis thaliana) Explore Q9SU72  Go to UniProtKB:  Q9SU72

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PAD4	B	541	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AXX17_At3g46840, AN1_LOCUS15608
UniProt
Find proteins for A0A178V847 (Arabidopsis thaliana) Explore A0A178V847  Go to UniProtKB:  A0A178V847

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable disease resistance protein At5g04720	C	811	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g04720, MUK11.4, T1E3.80
UniProt
Find proteins for Q9LZ25 (Arabidopsis thaliana) Explore Q9LZ25  Go to UniProtKB:  Q9LZ25

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
RP5 (Subject of Investigation/LOI)	E [auth A]	5-O-phosphono-beta-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-TXICZTDVSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Wang, H., Tan, J., Cui, X., Song, S., Yan, C., Qi, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release