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- EMDB-39384: EDS1-SAG101-NRG1C heterotrimer -

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Basic information

Entry
Database: EMDB / ID: EMD-39384
TitleEDS1-SAG101-NRG1C heterotrimer
Map data
Sample
  • Complex: EDS1-SAG101-NRG1C heterotrimer
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66890
  • 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 1.3 / 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, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / defense response to other organism / 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, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / defense response to other organism / 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 / cytosol / cytoplasm
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)
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_39384.png

Downloads & links

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Map

FileDownload / File: emd_39384.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

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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-0.24765947 - 0.67093515
Average (Standard dev.)0.0012314615 (±0.023567155)
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_39384_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_39384_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_39384_half_map_2.map
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Sample components

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Entire : EDS1-SAG101-NRG1C heterotrimer

EntireName: EDS1-SAG101-NRG1C heterotrimer
Components
  • Complex: EDS1-SAG101-NRG1C heterotrimer
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66890
  • 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-NRG1C heterotrimer

SupramoleculeName: EDS1-SAG101-NRG1C 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 At5g66890

MacromoleculeName: Probable disease resistance protein At5g66890 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 47.602734 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MNSNSIQSFD ALPHNLRECF LDMASFLEDQ RIIASTIIDL WSASYGKEGM NNLQDLASRN LLKLLPIGRN EYEDGFYNEL LVKQDNVLR EFAINQCLKE SSSIFERKRL NLEIQDNKFP NWCLNPKQPI VINASLFSIS TDDSFASSWF EMDCPNVEAL V LNISSSNY ...String:
MNSNSIQSFD ALPHNLRECF LDMASFLEDQ RIIASTIIDL WSASYGKEGM NNLQDLASRN LLKLLPIGRN EYEDGFYNEL LVKQDNVLR EFAINQCLKE SSSIFERKRL NLEIQDNKFP NWCLNPKQPI VINASLFSIS TDDSFASSWF EMDCPNVEAL V LNISSSNY ALPNFIATMK ELKVVIIINH GLEPAKLTNL SCLSSLPNLK RIRFEKVSIS LLDIPKLGLK SLEKLSLWFC HV VDALNEL EDVSETLQSL QEIEIDYCYN LDELPYWISQ VVSLKKLSVT NCNKLCRVIE AIGDLRDLET LRLSSCASLL ELP ETIDRL DNLRFLDVSG GFQLKNLPLE IGKLKKLEKI SMKDCYRCEL PDSVKNLENL EVKCDEDTAF LWKILKPEMK NLTI TEEKT EHNLNLLQLF

UniProtKB: Probable disease resistance protein At5g66890

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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: 161763
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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