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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9JBN

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SU72
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PAD4	B	541	Arabidopsis thaliana	Mutation(s): 0 Gene Names: AXX17_At3g46840, AN1_LOCUS15608 EC: 2.3.1
UniProt
Find proteins for Q9S745 (Arabidopsis thaliana) Explore Q9S745 Go to UniProtKB: Q9S745
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S745
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LZ25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
RP5 (Subject of Investigation/LOI) Query on RP5 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	5-O-phosphono-beta-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-TXICZTDVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.