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Open data
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Basic information
Entry | Database: PDB / ID: 7xey | ||||||
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Title | EDS1-PAD4 complexed with pRib-ADP | ||||||
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![]() | PLANT PROTEIN / EDS1 / PAD4 / pRib-ADP | ||||||
Function / homology | ![]() 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 / defense response to insect / negative regulation of ethylene-activated signaling pathway ...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 / defense response to insect / negative regulation of ethylene-activated signaling pathway / leaf abscission / 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 / ethylene-activated signaling pathway / leaf senescence / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, S. / Jia, A. / Xiao, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.6 KB | Display | ![]() |
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PDB format | ![]() | 198.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 46.9 KB | Display | |
Data in CIF | ![]() | 68.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xddC ![]() 4nfuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 71784.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 61054.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9S745, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
-Sugars , 1 types, 1 molecules ![](data/chem/img/RP5.gif)
#4: Sugar | ChemComp-RP5 / |
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-Non-polymers , 3 types, 612 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-TRS / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.53 Å2 / Biso mean: 39.8435 Å2 / Biso min: 15.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→46.07 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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