8YL6 | pdb_00008yl6

EDS1-SAG101-NRG1A L134E heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb8YL6/pdb
• EM Map EMD-39383: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Arabidopsis thaliana
• Mutation(s): Yes 


• Deposited: 2024-03-05 Released: 2025-01-29 
• Deposition Author(s): Wu, X.X., Xiao, Y.Y., Wang, Z.Z., Zhang, Y., Wan, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activation and inhibition mechanisms of a plant helper NLR.

Xiao, Y., Wu, X., Wang, Z., Ji, K., Zhao, Y., Zhang, Y., Wan, L.

(2025) Nature 639: 438-446

• PubMed: 39939758 
• DOI: https://doi.org/10.1038/s41586-024-08517-3
• Primary Citation Related Structures: 
  8YL6, 8YL7


• PubMed Abstract: 
  

  Plant nucleotide-binding leucine-rich repeat (NLR) receptors sense pathogen effectors and form resistosomes to confer immunity ¹ . Some sensor NLR resistosomes produce small molecules to induce formation of a heterotrimer complex with two lipase-like proteins, EDS1 and SAG101, and a helper NLR called NRG1 (refs. ^2,3 ). Activation of sensor NLR resistosomes also triggers NRG1 oligomerization and resistosome formation at the plasma membrane ^4,5 . We demonstrate that the Arabidopsis AtEDS1-AtSAG101-AtNRG1A heterotrimer formation is stabilized by the AtNRG1A loss-of-oligomerization mutant L134E ^5,6 . We report structures of AtEDS1-AtSAG101-AtNRG1A L134E and AtEDS1-AtSAG101-AtNRG1C heterotrimers with similar assembly mechanisms. AtNRG1A signalling is activated by the interaction with the AtEDS1-AtSAG101 heterodimer in complex with their small-molecule ligand. The truncated AtNRG1C maintains core interacting domains of AtNRG1A but develops further interactions with AtEDS1-AtSAG101 to outcompete AtNRG1A. Moreover, AtNRG1C lacks an N-terminal signalling domain and shows nucleocytoplasmic localization, facilitating its sequestration of AtEDS1-AtSAG101, which is also nucleocytoplasmic. Our study shows the activation and inhibition mechanisms of a plant helper NLR.

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Organizational Affiliation: 
• State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Plant Carbon Capture, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].
Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].

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: 227.35 kDa 
• Atom Count: 10,632 
• Modeled Residue Count: 1,439 
• Deposited Residue Count: 1,969 
• 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
Senescence-associated carboxylesterase 101	B	537	Arabidopsis thaliana	Mutation(s): 0  Gene Names: SAG101, At5g14930, F2G14.50 EC: 3.1.1.1
UniProt
Find proteins for Q4F883 (Arabidopsis thaliana) Explore Q4F883  Go to UniProtKB:  Q4F883

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable disease resistance protein At5g66900	C	809	Arabidopsis thaliana	Mutation(s): 1  Gene Names: At5g66900, MUD21.16
UniProt
Find proteins for Q9FKZ1 (Arabidopsis thaliana) Explore Q9FKZ1  Go to UniProtKB:  Q9FKZ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L15	D [auth A]	[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C25 H37 N10 O26 P5 BLHBPWIRUPJXKW-VIUUMBSUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Wu, X.X., Xiao, Y.Y., Wang, Z.Z., Zhang, Y., Wan, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270304
Chinese Academy of Sciences	China	XDB27040214

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Data collection, Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references