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- EMDB-33233: Cryo-EM structure of EDS1 and SAG101 with ATP-APDR -

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Basic information

Entry
Database: EMDB / ID: EMD-33233
TitleCryo-EM structure of EDS1 and SAG101 with ATP-APDR
Map data
Sample
  • Complex: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
  • Ligand: ISOPROPYL ALCOHOL
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


positive regulation of defense response to oomycetes / aerenchyma formation / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium ...positive regulation of defense response to oomycetes / aerenchyma formation / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium / lipase activity / carboxylesterase / carboxylesterase activity / regulation of hydrogen peroxide metabolic process / 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 / membrane / nucleus / 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. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Senescence-associated carboxylesterase 101 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsHuang SJ / Jia AL / Han ZF / Chai JJ
Funding support China, Germany, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Alexander von Humboldt Foundation Germany
CitationJournal: Science / Year: 2022
Title: TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity.
Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / ...Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / Ertong Li / Shoucai Ma / Dongli Yu / Jan Gebauer / Ulrich Baumann / Xiaohui Liu / Zhifu Han / Junbiao Chang / Jane E Parker / Jijie Chai /
Abstract: Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease ...Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners, Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) produces signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR subclasses. In this work, we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) through ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of ADPr-ATP or di-ADPR allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta. Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.
History
DepositionApr 18, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33233.png

Downloads & links

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Map

FileDownload / File: emd_33233.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.033766057 - 0.06498281
Average (Standard dev.)8.654378e-05 (±0.0014127793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33233_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33233_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of EDS1 and SAG101 with molecule ATP-ADPR

EntireName: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR
Components
  • Complex: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR
    • Protein or peptide: Protein EDS1
    • Protein or peptide: Senescence-associated carboxylesterase 101
  • Ligand: ISOPROPYL ALCOHOL
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR

SupramoleculeName: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis (plant)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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 (plant)
Molecular weightTheoretical: 71.784195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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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 (plant)
Molecular weightTheoretical: 62.153391 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #3: ISOPROPYL ALCOHOL

MacromoleculeName: ISOPROPYL ALCOHOL / type: ligand / ID: 3 / Number of copies: 1 / Formula: IPA
Molecular weightTheoretical: 60.095 Da
Chemical component information

ChemComp-IPA:
ISOPROPYL ALCOHOL / alkaloid*YM / Isopropyl alcohol

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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 / Adenosine triphosphate

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 652337

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