+Open data
-Basic information
Entry | Database: PDB / ID: 7xjp | |||||||||
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Title | Cryo-EM structure of EDS1 and SAG101 with ATP-APDR | |||||||||
Components |
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Keywords | PLANT PROTEIN / NLR / Plant immune signaling | |||||||||
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 / carboxylesterase / lipase activity / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis (plant) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å | |||||||||
Authors | Huang, S.J. / Jia, A.L. / Han, Z.F. / Chai, J.J. | |||||||||
Funding support | China, Germany, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xjp.cif.gz | 278.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xjp.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 7xjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xjp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7xjp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7xjp_validation.xml.gz | 41 KB | Display | |
Data in CIF | 7xjp_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/7xjp ftp://data.pdbj.org/pub/pdb/validation_reports/xj/7xjp | HTTPS FTP |
-Related structure data
Related structure data | 33233MC 7xozC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 71784.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis (plant) / Gene: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SU72 |
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#2: Protein | Mass: 62153.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis (plant) / Gene: SAG101, At5g14930, F2G14.50 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4F883, carboxylesterase |
#3: Chemical | ChemComp-IPA / |
#4: Chemical | ChemComp-APR / |
#5: Chemical | ChemComp-ATP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis (plant) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 652337 / Symmetry type: POINT | ||||||||||||||||||||||||
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