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- PDB-8yn1: Cryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP) -

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Basic information

Entry
Database: PDB / ID: 8yn1
TitleCryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP)
Components
  • Probable disease resistance protein At5g66900
  • Protein EDS1
  • Senescence-associated carboxylesterase 101
KeywordsPLANT PROTEIN/HYDROLASE / Plant immunity / ETI / NRG1A / EDS1 / SAG101 / ADPr-ATP / PLANT PROTEIN / PLANT PROTEIN-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, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium ...positive regulation of defense response to oomycetes / positive regulation of leaf senescence / 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 / 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 / endomembrane system / chloroplast / defense response / ADP binding / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Senescence-associated carboxylesterase 101-like / 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) / Apoptotic protease-activating factors, helical domain ...Senescence-associated carboxylesterase 101-like / 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) / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Lipases, serine active site. / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADENOSINE-5'-TRIPHOSPHATE / Senescence-associated carboxylesterase 101 / Probable disease resistance protein At5g66900 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsHuang, S. / Xiao, Y. / Chai, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2025
Title: Balanced plant helper NLR activation by a modified host protein complex.
Authors: Shijia Huang / Junli Wang / Ridan Song / Aolin Jia / Yu Xiao / Yue Sun / Lin Wang / Dennis Mahr / Zhongshou Wu / Zhifu Han / Xin Li / Jane E Parker / Jijie Chai /
Abstract: Nucleotide-binding leucine-rich repeat (NLR) receptors play crucial roles in plant immunity by sensing pathogen effectors. In Arabidopsis, certain sensor NLRs function as NADases to catalyse the ...Nucleotide-binding leucine-rich repeat (NLR) receptors play crucial roles in plant immunity by sensing pathogen effectors. In Arabidopsis, certain sensor NLRs function as NADases to catalyse the production of second messengers, which can be recognized by enhanced disease susceptibility 1 (EDS1) with its partner senescence-associated gene 101 (SAG101), to activate helper NLR N requirement gene 1 (NRG1). A cryoelectron microscopy structure shows that second-messenger-activated EDS1-SAG101 mainly contacts the leucine-rich repeat domain of NRG1A to mediate the formation of an induced EDS1-SAG101-NRG1A complex. Structural comparisons show that binding of a second messenger induces conformational changes in EDS1-SAG101, which are recognized by NRG1A, leading to its allosteric activation. We further show that an inhibitory NRG1 family member, NRG1C, efficiently outcompetes NRG1A for binding to second-messenger-activated EDS1-SAG101. These findings uncover mechanisms for NRG1A activation through its recognition of a modified host EDS1-SAG101 complex, and NRG1A inhibition by NRG1C through sequestration of the activated EDS1-SAG101, thus shedding light on the activation and constraint of a central plant immune response system.
History
DepositionMar 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: 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 At5g66900
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,9225
Polymers178,8553
Non-polymers1,0662
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: 70715.953 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SU72
#2: Protein Senescence-associated carboxylesterase 101


Mass: 61677.875 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4F883, carboxylesterase
#3: Protein Probable disease resistance protein At5g66900


Mass: 46461.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66900, MUD21.16 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FKZ1
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
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: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis (plant)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275262 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00812442
ELECTRON MICROSCOPYf_angle_d0.83316799
ELECTRON MICROSCOPYf_dihedral_angle_d13.9011698
ELECTRON MICROSCOPYf_chiral_restr0.0511858
ELECTRON MICROSCOPYf_plane_restr0.0062127

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