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- EMDB-39411: Cryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP) -

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Basic information

Entry
Database: EMDB / ID: EMD-39411
TitleCryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP)
Map data
Sample
  • Complex: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66900
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPlant 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
Senescence-associated carboxylesterase 101 / Probable disease resistance protein At5g66900 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsHuang S / Xiao Y / Chai J
Funding support China, 1 items
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, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_39411.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 240 pix.
= 204. Å
0.85 Å/pix.
x 240 pix.
= 204. Å
0.85 Å/pix.
x 240 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.101961106 - 0.1828354
Average (Standard dev.)0.00030116204 (±0.0042365645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39411_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_39411_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)

EntireName: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
Components
  • Complex: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
    • Protein or peptide: Probable disease resistance protein At5g66900
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)

SupramoleculeName: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis (plant)

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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: 70.715953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AFEALTGING DLITRSWSAS KQAYLTERYH KEEAGAVVIF AFQPSFSEKD FFDPDNKSSF GEIKLNRVQF PCMRKIGKGD VATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL V GDSIFSHA ...String:
AFEALTGING DLITRSWSAS KQAYLTERYH KEEAGAVVIF AFQPSFSEKD FFDPDNKSSF GEIKLNRVQF PCMRKIGKGD VATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL V GDSIFSHA LGREKWSRFF VNFVSRFDIV PRIMLARKAS VEETLPHVLA QLDPRKSSVQ ESEQRITEFY TRVMRDTSTV AN QAVCELT GSAEAFLETL SSFLELSPYR PAGTFVFSTE KRLVAVNNSD AILQMLFYTS QASDEQEWSL IPFRSIRDHH SYE ELVQSM GKKLFNHLDG ENSIESTLND LGVSTRGRQY VQAALEEEKK RVENQKKIIQ VIEQERFLKK LAWIEDEYKP KCQA HKNGY YDSFKVSNEE NDFKANVKRA ELAGVFDEVL GLMKKCQLPD EFEGDIDWIK LATRYRRLVE PLDIANYHRH LKNED TGPY MKRGRPTRYI YAQRGYEHYI LKPNGMIAED VFWNKVNGLN LGLQLEEIQE TLKNSGSECG SCFWAEVEEL KGKPYE EVE VRVKTLEGML GEWITDGEVD DKEIFLEGST FRKWWITLPK NHKSHSPLRD Y

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: 61.677875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SSSSLKGSAL GKLVVTSGLL HSSWSKILEI HNPPYSNHDP GLQVSKKKKD SGLEFQIHRE EKFTLVVFSA PPICRSSSSD STLLHVKDK ENPFPFLCSE NNPSFSLHTP AFNLFTSAST SLTYLKSELL QTLKSEKPVI ITGAALGGSV ASLYTLWLLE T IEPTLKRP ...String:
SSSSLKGSAL GKLVVTSGLL HSSWSKILEI HNPPYSNHDP GLQVSKKKKD SGLEFQIHRE EKFTLVVFSA PPICRSSSSD STLLHVKDK ENPFPFLCSE NNPSFSLHTP AFNLFTSAST SLTYLKSELL QTLKSEKPVI ITGAALGGSV ASLYTLWLLE T IEPTLKRP LCITFGSPLI GDASLQQILE NSVRNSCFLH VVSAQTRIKM DFFKPFGTFL ICFDSGCVCI EDHVAVTELL NG VHDSGLV DYSQVLNRLD QSMLSLADSR LIPEDVIKGI EKRAEMKNLR FDMMFKKLND MKISMAYIEW YKKKCKEVKI GYY DRFKTQ LAFPSKEFDI NIKNHHKSEL NRFWKSVVEE VERRPQSDAS ILKRRFLFSG NNYRRMIEPL DIAEYYLEGR KEYR TTGRS HHYVMLEKWF GMESILIEKE RCKKRDLSDL LTFDSCFWAE VEDSLIVINQ LNTTVGMRDD VREVLTRKLV EFEGY VWEI ITKREVSPEI FLEESSFMKW WKEYKKIKGF NSSYLTEFMN TRKYESYGK

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: 46.461461 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SFDALDPNLK ECFLDMGSFL EDQKIRASVI IDMWVELYGK GSSILYMYLE DLASQNLLKL VPLGTNEHED GFYNDFLVTQ HDILRELAI CQSEFKENLE RKRLNLEILE NTFPDWCLNT INASLLSIST DDLFSSKWLE MDCPNVEALV LNLSSSDYAL P SFISGMKK ...String:
SFDALDPNLK ECFLDMGSFL EDQKIRASVI IDMWVELYGK GSSILYMYLE DLASQNLLKL VPLGTNEHED GFYNDFLVTQ HDILRELAI CQSEFKENLE RKRLNLEILE NTFPDWCLNT INASLLSIST DDLFSSKWLE MDCPNVEALV LNLSSSDYAL P SFISGMKK LKVLTITNHG FYPARLSNFS CLSSLPNLKR IRLEKVSITL LDIPQLQLSS LKKLSLVMCS FGEVFYDTED IV VSNALSK LQEIDIDYCY DLDELPYWIS EIVSLKTLSI TNCNKLSQLP EAIGNLSRLE VLRLCSSMNL SELPEATEGL SNL RFLDIS HCLGLRKLPQ EIGKLQNLKK ISMRKCSGCE LPESVTNLEN LEVKCDEETG LLWERLKPKM RNLRVQEEEI EHNL NLLQM F

UniProtKB: Probable disease resistance protein At5g66900

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Macromolecule #4: ADENOSINE-5-DIPHOSPHORIBOSE

MacromoleculeName: ADENOSINE-5-DIPHOSPHORIBOSE / type: ligand / ID: 4 / Number of copies: 1 / Formula: APR
Molecular weightTheoretical: 559.316 Da
Chemical component information

ChemComp-APR:
ADENOSINE-5-DIPHOSPHORIBOSE

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: PDB ENTRY
PDB model - PDB ID:
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275262
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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