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- PDB-7xey: EDS1-PAD4 complexed with pRib-ADP -

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Basic information

Entry
Database: PDB / ID: 7xey
TitleEDS1-PAD4 complexed with pRib-ADP
Components
  • Lipase-like PAD4
  • Protein EDS1
KeywordsPLANT PROTEIN / EDS1 / PAD4 / pRib-ADP
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 / regulation of salicylic acid mediated signaling pathway / positive regulation of salicylic acid mediated signaling pathway / negative regulation of ethylene-activated signaling pathway / regulation of jasmonic acid mediated signaling pathway / aerenchyma formation / EDS1 disease-resistance complex ...cellular response to trehalose stimulus / regulation of salicylic acid biosynthetic process / positive regulation of camalexin biosynthetic process / positive regulation of defense response to insect / regulation of salicylic acid mediated signaling pathway / positive regulation of salicylic acid mediated signaling pathway / negative regulation of ethylene-activated signaling pathway / regulation of jasmonic acid mediated signaling pathway / aerenchyma formation / EDS1 disease-resistance complex / defense response to insect / leaf abscission / response to insect / negative regulation of defense response / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / response to salicylic acid / leaf senescence / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium / ethylene-activated signaling pathway / 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 / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / 5-O-phosphono-beta-D-ribofuranose / Lipase-like PAD4 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHuang, S. / Jia, A. / Xiao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 10, 2022Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein EDS1
B: Lipase-like PAD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6185
Polymers132,8392
Non-polymers7793
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-27 kcal/mol
Surface area46620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.357, 91.863, 94.271
Angle α, β, γ (deg.)90.000, 111.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein EDS1 / Enhanced disease susceptibility 1


Mass: 71784.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SU72
#2: Protein Lipase-like PAD4 / Protein ENHANCED DISEASE SUSCEPTIBILITY 9 / Protein PHYTOALEXIN DEFICIENT 4 / AtPAD4


Mass: 61054.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAD4, EDS9, At3g52430, F22O6.190 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9S745, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 612 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.4, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 57868 / % possible obs: 98.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Χ2: 1.108 / Net I/σ(I): 5.2 / Num. measured all: 368298
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.29-2.334.50.69428500.7660.3530.7831.04298
2.33-2.375.20.65129190.80.3070.7231.00499.4
2.37-2.425.60.61229290.8510.2780.6741.01699.2
2.42-2.4760.57528450.890.2530.631.01298.9
2.47-2.526.40.54428900.90.2320.5931.03198.8
2.52-2.586.50.51229200.9180.2150.5561.00398.9
2.58-2.646.50.47928490.9290.2010.521.02898.5
2.64-2.726.50.41428820.9370.1740.451.08298
2.72-2.795.90.35128090.9490.1550.3851.07296
2.79-2.896.70.29928790.9610.1240.3241.05699
2.89-2.996.90.26129180.9730.1060.2821.09499.4
2.99-3.116.90.21629060.980.0880.2331.11199.5
3.11-3.256.90.17129360.9880.070.1851.11998.6
3.25-3.426.80.1428890.990.0570.1511.17398.4
3.42-3.636.30.11828110.9910.0510.1291.22995.8
3.63-3.926.80.128940.9950.0410.1081.34198.8
3.92-4.3170.07529600.9970.030.0811.23999.8
4.31-4.936.80.06329060.9970.0260.0681.22698.4
4.93-6.216.40.06428950.9970.0270.071.10697.2
6.21-506.60.04429810.9990.0190.0481.06598.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nfu

4nfu


Resolution: 2.29→46.07 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1992 3.45 %
Rwork0.1844 55769 -
obs0.186 57761 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.53 Å2 / Biso mean: 39.8435 Å2 / Biso min: 15.48 Å2
Refinement stepCycle: final / Resolution: 2.29→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 48 610 9755
Biso mean--30.12 38.33 -
Num. residues----1133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.340.31521280.25323767389593
2.34-2.410.3321380.24884016415499
2.41-2.480.3051510.22764004415599
2.48-2.560.24271400.22153992413299
2.56-2.650.29321460.22293992413899
2.65-2.760.26591420.21733949409198
2.76-2.880.26811310.20843974410598
2.88-3.030.2691480.211240414189100
3.03-3.220.26421450.20813993413899
3.22-3.470.2611530.19524003415698
3.47-3.820.20351240.17163948407297
3.82-4.380.21421530.153440774230100
4.38-5.510.18171460.14483974412097
5.51-46.070.16871470.14964039418697

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