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- EMDB-33144: Cryo-EM structure of EDS1 and PAD4 -

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Basic information

Entry
Database: EMDB / ID: EMD-33144
TitleCryo-EM structure of EDS1 and PAD4
Map data
Sample
  • Complex: Binary complex of EDS1 and PAD4
    • Complex: PAD4
      • Protein or peptide: Lipase-like PAD4
    • Complex: EDS1
      • Protein or peptide: Protein EDS1
Function / homology
Function and homology information


cellular response to trehalose stimulus / regulation of salicylic acid biosynthetic process / positive regulation of camalexin biosynthetic process / positive regulation of defense response to insect / aerenchyma formation / positive regulation of salicylic acid mediated signaling pathway / EDS1 disease-resistance complex / regulation of salicylic acid mediated signaling pathway / leaf abscission / defense response to insect ...cellular response to trehalose stimulus / regulation of salicylic acid biosynthetic process / positive regulation of camalexin biosynthetic process / positive regulation of defense response to insect / aerenchyma formation / positive regulation of salicylic acid mediated signaling pathway / EDS1 disease-resistance complex / regulation of salicylic acid mediated signaling pathway / leaf abscission / defense response to insect / negative regulation of ethylene-activated signaling pathway / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / response to insect / systemic acquired resistance / : / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to salicylic acid / leaf senescence / ethylene-activated signaling pathway / response to singlet oxygen / positive regulation of defense response to bacterium / lipase activity / regulation of hydrogen peroxide metabolic process / response to other organism / response to UV-C / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chloroplast / response to bacterium / lipid metabolic process / transferase activity / defense response to Gram-negative bacterium / response to hypoxia / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Lipase-like PAD4 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHuang SJ / Jia AL / Sun Y / 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: Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity.
Authors: Shijia Huang / Aolin Jia / Wen Song / Giuliana Hessler / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Shoucai Ma / Yu Xiao / Dongli Yu / Jiao Hou / Ruiqi Liu / ...Authors: Shijia Huang / Aolin Jia / Wen Song / Giuliana Hessler / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Shoucai Ma / Yu Xiao / Dongli Yu / Jiao Hou / Ruiqi Liu / Huanhuan Sun / Xiaohui Liu / Zhifu Han / Junbiao Chang / Jane E Parker / Jijie Chai /
Abstract: Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded nicotinamide adenine ...Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) activity for immune signaling. TIR-NLR signaling requires the helper NLRs N requirement gene 1 (NRG1), Activated Disease Resistance 1 (ADR1), and Enhanced Disease Susceptibility 1 (EDS1), which forms a heterodimer with each of its paralogs Phytoalexin Deficient 4 (PAD4) and Senescence-Associated Gene 101 (SAG101). Here, we show that TIR-containing proteins catalyze the production of 2'-(5''-phosphoribosyl)-5'-adenosine monophosphate (pRib-AMP) and diphosphate (pRib-ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP and pRib-ADP, which allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP and pRib-ADP as a missing link in TIR signaling through EDS1-PAD4 and as likely second messengers for plant immunity.
History
DepositionMar 26, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33144.png

Downloads & links

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Map

FileDownload / File: emd_33144.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.6746 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.023742046 - 0.043979436
Average (Standard dev.)8.419959e-05 (±0.001228214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 202.38 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33144_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_33144_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 PAD4

EntireName: Binary complex of EDS1 and PAD4
Components
  • Complex: Binary complex of EDS1 and PAD4
    • Complex: PAD4
      • Protein or peptide: Lipase-like PAD4
    • Complex: EDS1
      • Protein or peptide: Protein EDS1

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Supramolecule #1: Binary complex of EDS1 and PAD4

SupramoleculeName: Binary complex of EDS1 and PAD4 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: PAD4

SupramoleculeName: PAD4 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: EDS1

SupramoleculeName: EDS1 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Lipase-like PAD4

MacromoleculeName: Lipase-like PAD4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 60.693133 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: CRFETSELQA SVMISTPLFT DSWSSCNTAN CNGSIKIHDI AGITYVAIPA VSMIQLGNLV GLPVTGDVLF PGLSSDEPLP MVDAAILKL FLQLKIKEGL ELELLGKKLV VITGHSTGGA LAAFTALWLL SQSSPPSFRV FCITFGSPLL GNQSLSTSIS R SRLAHNFC ...String:
CRFETSELQA SVMISTPLFT DSWSSCNTAN CNGSIKIHDI AGITYVAIPA VSMIQLGNLV GLPVTGDVLF PGLSSDEPLP MVDAAILKL FLQLKIKEGL ELELLGKKLV VITGHSTGGA LAAFTALWLL SQSSPPSFRV FCITFGSPLL GNQSLSTSIS R SRLAHNFC HVVSIHDLVP RSSNEQFWPF GTYLFCSDKG GVCLDNAGSV RLMFNILNTT ATQNTEEHQR YGHYVFTLSH MF LKSRSFL GGSIPDNSYQ AGVALAVEAL GFSNDDTSGV LVKECIETAT RIVRAPILRS AELANELASV LPARLEIQWY KDR CDASEE QLGYYDFFKR YSLKRDFKVN MSRIRLAKFW DTVIKMVETN ELPFDFHLGK KWIYASQFYQ LLAEPLDIAN FYKN RDIKT GGHYLEGNRP KRYEVIDKWQ KGVKVPEECV RSRYASTTQD TCFWAKLEQA KEWLDEARKE SSDPQRRSLL REKIV PFES YANTLVTKKE VSLDVKAKNS SYSVWEANLK EFKCKMGYEN EIEMVVDESD AMET

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Macromolecule #2: Protein EDS1

MacromoleculeName: Protein EDS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
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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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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133202

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