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- EMDB-60520: RPS4-TIR induced At EDS1-PAD4-ADR1 heterotrimer -

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Basic information

Entry
Database: EMDB / ID: EMD-60520
TitleRPS4-TIR induced At EDS1-PAD4-ADR1 heterotrimer
Map data
Sample
  • Complex: At EDS1-PAD4-ADR1 heterotrimer by RPS4
    • Protein or peptide: Disease resistance protein ADR1
    • Protein or peptide: Isoform 1 of Protein EDS1
    • Protein or peptide: PAD4
  • Ligand: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate
KeywordsEffector-triggered immunity (ETI) / TNL signaling pathway / EDS1 / PAD4 / ADR1 / PLANT PROTEIN
Function / homology
Function and homology information


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 / lipase activity / regulation of hydrogen peroxide metabolic process / response to water deprivation ...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 / lipase activity / regulation of hydrogen peroxide metabolic process / response to water deprivation / response to other organism / chloroplast / defense response / ADP binding / lipid metabolic process / kinase activity / defense response to Gram-negative bacterium / response to hypoxia / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PAD4 / Disease resistance protein ADR1 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsXu WY / Zhang Y / Yu H / Wan L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: Activation of a helper NLR by plant and bacterial TIR immune signaling.
Authors: Hua Yu / Weiying Xu / Sisi Chen / Xiaoxian Wu / Weiwei Rao / Xiaoxiao Liu / Xiaoyan Xu / Jingqi Chen / Marc T Nishimura / Yu Zhang / Li Wan /
Abstract: Plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to initiate immune signaling. TIR ...Plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to initiate immune signaling. TIR domains across different kingdoms have NADase activities and can produce phosphoribosyl adenosine monophosphate/diphosphate (pRib-AMP/ADP) or cyclic ADPR (cADPR) isomers. The lipase-like proteins EDS1 and PAD4 transduce immune signals from sensor TIR-NLRs to a helper NLR called ADR1, which executes immune function. We report the structure and function of an EDS1-PAD4-ADR1 (EPA) heterotrimer in complex with pRib-AMP/ADP activated by plant or bacterial TIR signaling. 2'cADPR can be hydrolyzed into pRib-AMP and thus activate EPA signaling. Bacterial TIR domains producing 2'cADPR also activate EPA function. Our findings suggest that 2'cADPR may be the storage form of the unstable signaling molecule pRib-AMP.
History
DepositionJun 12, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60520.png

Downloads & links

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Map

FileDownload / File: emd_60520.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.25060308 - 0.76001453
Average (Standard dev.)0.003589307 (±0.028961418)
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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Half map: #2

Fileemd_60520_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_60520_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : At EDS1-PAD4-ADR1 heterotrimer by RPS4

EntireName: At EDS1-PAD4-ADR1 heterotrimer by RPS4
Components
  • Complex: At EDS1-PAD4-ADR1 heterotrimer by RPS4
    • Protein or peptide: Disease resistance protein ADR1
    • Protein or peptide: Isoform 1 of Protein EDS1
    • Protein or peptide: PAD4
  • Ligand: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate

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Supramolecule #1: At EDS1-PAD4-ADR1 heterotrimer by RPS4

SupramoleculeName: At EDS1-PAD4-ADR1 heterotrimer by RPS4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Disease resistance protein ADR1

MacromoleculeName: Disease resistance protein ADR1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 90.252016 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASFIDLFAG DITTQLLKLL ALVANTVYSC KGIAERLITM IRDVQPTIRE IQYSGAELSN HHQTQLGVFY EILEKARKLC EKVLRCNRW NLKHVYHANK MKDLEKQISR FLNSQILLFV LAEVCHLRVN GDRIERNMDR LLTERNDSLS FPETMMEIET V SDPEIQTV ...String:
MASFIDLFAG DITTQLLKLL ALVANTVYSC KGIAERLITM IRDVQPTIRE IQYSGAELSN HHQTQLGVFY EILEKARKLC EKVLRCNRW NLKHVYHANK MKDLEKQISR FLNSQILLFV LAEVCHLRVN GDRIERNMDR LLTERNDSLS FPETMMEIET V SDPEIQTV LELGKKKVKE MMFKFTDTHL FGISGMSGSG KTTLAIELSK DDDVRGLFKN KVLFLTVSRS PNFENLESCI RE FLYDGVH QRKLVILDDV WTRESLDRLM SKIRGSTTLV VSRSKLADPR TTYNVELLKK DEAMSLLCLC AFEQKSPPSP FNK YLVKQV VDECKGLPLS LKVLGASLKN KPERYWEGVV KRLLRGEAAD ETHESRVFAH MEESLENLDP KIRDCFLDMG AFPE DKKIP LDLLTSVWVE RHDIDEETAF SFVLRLADKN LLTIVNNPRF GDVHIGYYDV FVTQHDVLRD LALHMSNRVD VNRRE RLLM PKTEPVLPRE WEKNKDEPFD AKIVSLHTGE MDEMNWFDMD LPKAEVLILN FSSDNYVLPP FIGKMSRLRV LVIINN GMS PARLHGFSIF ANLAKLRSLW LKRVHVPELT SCTIPLKNLH KIHLIFCKVK NSFVQTSFDI SKIFPSLSDL TIDHCDD LL ELKSIFGITS LNSLSITNCP RILELPKNLS NVQSLERLRL YACPELISLP VEVCELPCLK YVDISQCVSL VSLPEKFG K LGSLEKIDMR ECSLLGLPSS VAALVSLRHV ICDEETSSMW EMVKKVVPEL CIEVAKKCFT VDWLDD

UniProtKB: Disease resistance protein ADR1

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Macromolecule #2: Isoform 1 of Protein EDS1

MacromoleculeName: Isoform 1 of 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

UniProtKB: Protein EDS1

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Macromolecule #3: PAD4

MacromoleculeName: PAD4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 61.054504 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDDCRFETSE LQASVMISTP LFTDSWSSCN TANCNGSIKI HDIAGITYVA IPAVSMIQLG NLVGLPVTGD VLFPGLSSDE PLPMVDAAI LKLFLQLKIK EGLELELLGK KLVVITGHST GGALAAFTAL WLLSQSSPPS FRVFCITFGS PLLGNQSLST S ISRSRLAH ...String:
MDDCRFETSE LQASVMISTP LFTDSWSSCN TANCNGSIKI HDIAGITYVA IPAVSMIQLG NLVGLPVTGD VLFPGLSSDE PLPMVDAAI LKLFLQLKIK EGLELELLGK KLVVITGHST GGALAAFTAL WLLSQSSPPS FRVFCITFGS PLLGNQSLST S ISRSRLAH NFCHVVSIHD LVPRSSNEQF WPFGTYLFCS DKGGVCLDNA GSVRLMFNIL NTTATQNTEE HQRYGHYVFT LS HMFLKSR SFLGGSIPDN SYQAGVALAV EALGFSNDDT SGVLVKECIE TATRIVRAPI LRSAELANEL ASVLPARLEI QWY KDRCDA SEEQLGYYDF FKRYSLKRDF KVNMSRIRLA KFWDTVIKMV ETNELPFDFH LGKKWIYASQ FYQLLAEPLD IANF YKNRD IKTGGHYLEG NRPKRYEVID KWQKGVKVPE ECVRSRYAST TQDTCFWAKL EQAKEWLDEA RKESSDPQRR SLLRE KIVP FESYANTLVT KKEVSLDVKA KNSSYSVWEA NLKEFKCKMG YENEIEMVVD ESDAMET

UniProtKB: PAD4

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Macromolecule #4: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxi...

MacromoleculeName: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1D8A
Molecular weightTheoretical: 639.296 Da

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
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: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 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: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150167
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8zw9:
RPS4-TIR induced At EDS1-PAD4-ADR1 heterotrimer

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