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- EMDB-39383: EDS1-SAG101-NRG1A L134E heterotrimer -

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Entry
Database: EMDB / ID: EMD-39383
TitleEDS1-SAG101-NRG1A L134E heterotrimer
Map data
Sample
  • Complex: EDS1-SAG101-NRG1A L134E heterotrimer
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66900
  • Ligand: [[(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
KeywordsEffector-triggered immunity (ETI) / Enhanced Disease Susceptibility1 / Senescence-Associated Gene101 / N Required Gene 1.1 / 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 / positive regulation of defense response to bacterium / response to singlet oxygen / plant-type hypersensitive response ...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 / positive regulation of defense response to bacterium / response to singlet oxygen / plant-type hypersensitive response / lipase activity / carboxylesterase / regulation of hydrogen peroxide metabolic process / carboxylesterase activity / lipid catabolic process / positive regulation of defense response to virus by host / endomembrane system / chloroplast / lipid metabolic process / defense response / ADP binding / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / ATP binding / membrane / nucleus / cytoplasm / cytosol
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
Senescence-associated carboxylesterase 101 / Probable disease resistance protein At5g66900 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWu XX / Xiao YY / Wang ZZ / Zhang Y / Wan L
Funding support China, 2 items
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, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39383.png

Downloads & links

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Map

FileDownload / File: emd_39383.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.49000543 - 0.98798347
Average (Standard dev.)0.0032342176 (±0.027891751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39383_additional_1.map
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Half map: #2

Fileemd_39383_half_map_1.map
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Half map: #1

Fileemd_39383_half_map_2.map
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Sample components

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Entire : EDS1-SAG101-NRG1A L134E heterotrimer

EntireName: EDS1-SAG101-NRG1A L134E heterotrimer
Components
  • Complex: EDS1-SAG101-NRG1A L134E heterotrimer
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66900
  • Ligand: [[(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

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Supramolecule #1: EDS1-SAG101-NRG1A L134E heterotrimer

SupramoleculeName: EDS1-SAG101-NRG1A L134E heterotrimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein EDS1

MacromoleculeName: Protein EDS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 71.784195 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ...String:
MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ALGREKWSRF FVNFVSRFDI VPRIMLARKA SVEETLPHVL AQLDPRKSSV QESEQRITEF YTRVMRDTST VA NQAVCEL TGSAEAFLET LSSFLELSPY RPAGTFVFST EKRLVAVNNS DAILQMLFYT SQASDEQEWS LIPFRSIRDH HSY EELVQS MGKKLFNHLD GENSIESTLN DLGVSTRGRQ YVQAALEEEK KRVENQKKII QVIEQERFLK KLAWIEDEYK PKCQ AHKNG YYDSFKVSNE ENDFKANVKR AELAGVFDEV LGLMKKCQLP DEFEGDIDWI KLATRYRRLV EPLDIANYHR HLKNE DTGP YMKRGRPTRY IYAQRGYEHY ILKPNGMIAE DVFWNKVNGL NLGLQLEEIQ ETLKNSGSEC GSCFWAEVEE LKGKPY EEV EVRVKTLEGM LGEWITDGEV DDKEIFLEGS TFRKWWITLP KNHKSHSPLR DYMMDEITDT

UniProtKB: Protein EDS1

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Macromolecule #2: Senescence-associated carboxylesterase 101

MacromoleculeName: Senescence-associated carboxylesterase 101 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: carboxylesterase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 62.153391 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MESSSSLKGS ALGKLVVTSG LLHSSWSKIL EIHNPPYSNH DPGLQVSKKK KDSGLEFQIH REEKFTLVVF SAPPICRSSS SDSTLLHVK DKENPFPFLC SENNPSFSLH TPAFNLFTSA STSLTYLKSE LLQTLKSEKP VIITGAALGG SVASLYTLWL L ETIEPTLK ...String:
MESSSSLKGS ALGKLVVTSG LLHSSWSKIL EIHNPPYSNH DPGLQVSKKK KDSGLEFQIH REEKFTLVVF SAPPICRSSS SDSTLLHVK DKENPFPFLC SENNPSFSLH TPAFNLFTSA STSLTYLKSE LLQTLKSEKP VIITGAALGG SVASLYTLWL L ETIEPTLK RPLCITFGSP LIGDASLQQI LENSVRNSCF LHVVSAQTRI KMDFFKPFGT FLICFDSGCV CIEDHVAVTE LL NGVHDSG LVDYSQVLNR LDQSMLSLAD SRLIPEDVIK GIEKRAEMKN LRFDMMFKKL NDMKISMAYI EWYKKKCKEV KIG YYDRFK TQLAFPSKEF DINIKNHHKS ELNRFWKSVV EEVERRPQSD ASILKRRFLF SGNNYRRMIE PLDIAEYYLE GRKE YRTTG RSHHYVMLEK WFGMESILIE KERCKKRDLS DLLTFDSCFW AEVEDSLIVI NQLNTTVGMR DDVREVLTRK LVEFE GYVW EIITKREVSP EIFLEESSFM KWWKEYKKIK GFNSSYLTEF MNTRKYESYG KSQ

UniProtKB: Senescence-associated carboxylesterase 101

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Macromolecule #3: Probable disease resistance protein At5g66900

MacromoleculeName: Probable disease resistance protein At5g66900 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 92.368734 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MNDWASLGIG SIGEAVFSKL LKVVIDEAKK FKAFKPLSKD LVSTMEILFP LTQKIDSMQK ELDFGVKELK ELRDTIERAD VAVRKFPRV KWYEKSKYTR KIERINKDML KFCQIDLQLL QHRNQLTLLG LTGNEVNSVD GLSKRMDLLS VPAPVFRDLC S VPKLDKVI ...String:
MNDWASLGIG SIGEAVFSKL LKVVIDEAKK FKAFKPLSKD LVSTMEILFP LTQKIDSMQK ELDFGVKELK ELRDTIERAD VAVRKFPRV KWYEKSKYTR KIERINKDML KFCQIDLQLL QHRNQLTLLG LTGNEVNSVD GLSKRMDLLS VPAPVFRDLC S VPKLDKVI VGLDWPLGEL KKRLLDDSVV TLVVSAPPGC GKTTLVSRLC DDPDIKGKFK HIFFNVVSNT PNFRVIVQNL LQ HNGYNAL TFENDSQAEV GLRKLLEELK ENGPILLVLD DVWRGADSFL QKFQIKLPNY KILVTSRFDF PSFDSNYRLK PLE DDDARA LLIHWASRPC NTSPDEYEDL LQKILKRCNG FPIVIEVVGV SLKGRSLNTW KGQVESWSEG EKILGKPYPT VLEC LQPSF DALDPNLKEC FLDMGSFLED QKIRASVIID MWVELYGKGS SILYMYLEDL ASQNLLKLVP LGTNEHEDGF YNDFL VTQH DILRELAICQ SEFKENLERK RLNLEILENT FPDWCLNTIN ASLLSISTDD LFSSKWLEMD CPNVEALVLN LSSSDY ALP SFISGMKKLK VLTITNHGFY PARLSNFSCL SSLPNLKRIR LEKVSITLLD IPQLQLSSLK KLSLVMCSFG EVFYDTE DI VVSNALSKLQ EIDIDYCYDL DELPYWISEI VSLKTLSITN CNKLSQLPEA IGNLSRLEVL RLCSSMNLSE LPEATEGL S NLRFLDISHC LGLRKLPQEI GKLQNLKKIS MRKCSGCELP ESVTNLENLE VKCDEETGLL WERLKPKMRN LRVQEEEIE HNLNLLQMF

UniProtKB: Probable disease resistance protein At5g66900

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Macromolecule #4: [[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R}...

MacromoleculeName: [[(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- ...Name: [[(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
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1L15
Molecular weightTheoretical: 1.048481 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142555
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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