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- PDB-8yl7: EDS1-SAG101-NRG1C heterotrimer -

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Basic information

Entry
Database: PDB / ID: 8yl7
TitleEDS1-SAG101-NRG1C heterotrimer
Components
  • Probable disease resistance protein At5g66890
  • Protein EDS1
  • Senescence-associated carboxylesterase 101
KeywordsIMMUNE SYSTEM/HYDROLASE / Effector-triggered immunity (ETI) / Enhanced Disease Susceptibility1 / Senescence-Associated Gene101 / N Required Gene 1.3 / IMMUNE SYSTEM / IMMUNE SYSTEM-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of defense response to oomycetes / positive regulation of leaf senescence / aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / defense response to other organism / plant-type hypersensitive response / response to singlet oxygen ...positive regulation of defense response to oomycetes / positive regulation of leaf senescence / aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / defense response to other organism / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium / lipase activity / carboxylesterase / regulation of hydrogen peroxide metabolic process / carboxylesterase activity / carboxylic ester hydrolase activity / lipid catabolic process / positive regulation of defense response to virus by host / chloroplast / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Senescence-associated carboxylesterase 101-like / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily ...Senescence-associated carboxylesterase 101-like / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Senescence-associated carboxylesterase 101 / Probable disease resistance protein At5g66890 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWu, X.X. / Xiao, Y.Y. / Wang, Z.Z. / Zhang, Y. / Wan, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270304 China
Chinese Academy of SciencesXDB27040214 China
CitationJournal: Nature / Year: 2025
Title: Activation and inhibition mechanisms of a plant helper NLR.
Authors: Yinyan Xiao / Xiaoxian Wu / Zaiqing Wang / Kexin Ji / Yang Zhao / Yu Zhang / Li Wan /
Abstract: Plant nucleotide-binding leucine-rich repeat (NLR) receptors sense pathogen effectors and form resistosomes to confer immunity. Some sensor NLR resistosomes produce small molecules to induce ...Plant nucleotide-binding leucine-rich repeat (NLR) receptors sense pathogen effectors and form resistosomes to confer immunity. 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. ). Activation of sensor NLR resistosomes also triggers NRG1 oligomerization and resistosome formation at the plasma membrane. We demonstrate that the Arabidopsis AtEDS1-AtSAG101-AtNRG1A heterotrimer formation is stabilized by the AtNRG1A loss-of-oligomerization mutant L134E. 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.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: 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: Senescence-associated carboxylesterase 101
C: Probable disease resistance protein At5g66890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,5894
Polymers181,5403
Non-polymers1,0481
Water00
1


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

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Components

#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: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SU72
#2: Protein Senescence-associated carboxylesterase 101


Mass: 62153.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SAG101, At5g14930, F2G14.50 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q4F883, carboxylesterase
#3: Protein Probable disease resistance protein At5g66890


Mass: 47602.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66890, MUD21.15 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKZ2
#4: Chemical ChemComp-A1L15 / [[(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 / ADPr-ATP


Mass: 1048.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H37N10O26P5 / Feature type: SUBJECT OF INVESTIGATION
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-SAG101-NRG1C heterotrimer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161763 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 168.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008411093
ELECTRON MICROSCOPYf_angle_d0.350915051
ELECTRON MICROSCOPYf_chiral_restr0.12511719
ELECTRON MICROSCOPYf_plane_restr0.00191923
ELECTRON MICROSCOPYf_dihedral_angle_d10.5056660

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