+Open data
-Basic information
Entry | Database: PDB / ID: 7xoz | |||||||||
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Title | Crystal structure of RPPT-TIR | |||||||||
Components | (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase) x 2 | |||||||||
Keywords | HYDROLASE / NLR / Plant Protein / Plant immune signaling | |||||||||
Function / homology | Function and homology information ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / ADP binding / defense response / signal transduction Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | |||||||||
Authors | Song, W. / Jia, A. / Huang, S. / Chai, J. | |||||||||
Funding support | Germany, China, 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 | 7xoz.cif.gz | 384.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xoz.ent.gz | 319.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xoz_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7xoz_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7xoz_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 7xoz_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/7xoz ftp://data.pdbj.org/pub/pdb/validation_reports/xo/7xoz | HTTPS FTP |
-Related structure data
Related structure data | 7xjpC 7crcS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 18936.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AN1_LOCUS14779 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: A0A654FE24, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase #2: Protein | Mass: 18946.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AN1_LOCUS14764 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A654FCP3 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion Details: 20 % w/v polyethylene glycol 3000 (PEG3000), 100 mM HEPES pH 7.5, 200 mM sodium |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→39.12 Å / Num. obs: 24611 / % possible obs: 98.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 49.84 Å2 / Rpim(I) all: 0.142 / Rrim(I) all: 0.293 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.52→2.61 Å / Num. unique obs: 2370 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CRC Resolution: 2.52→39.12 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→39.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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