+Open data
-Basic information
Entry | Database: PDB / ID: 7dfv | |||||||||
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Title | Cryo-EM structure of plant NLR RPP1 tetramer core part | |||||||||
Components | NAD+ hydrolase (NADase) | |||||||||
Keywords | PLANT PROTEIN / NADase / ETI / HR | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Ma, S.C. / Lapin, D. / Liu, L. / Sun, Y. / Song, W. / Zhang, X.X. / Logemann, E. / Yu, D.L. / Wang, J. / Jirschitzka, J. ...Ma, S.C. / Lapin, D. / Liu, L. / Sun, Y. / Song, W. / Zhang, X.X. / Logemann, E. / Yu, D.L. / Wang, J. / Jirschitzka, J. / Han, Z.F. / SchulzeLefert, P. / Parker, J.E. / Chai, J.J. | |||||||||
Funding support | China, Germany, 2items
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Citation | Journal: Science / Year: 2020 Title: Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Authors: Shoucai Ma / Dmitry Lapin / Li Liu / Yue Sun / Wen Song / Xiaoxiao Zhang / Elke Logemann / Dongli Yu / Jia Wang / Jan Jirschitzka / Zhifu Han / Paul Schulze-Lefert / Jane E Parker / Jijie Chai / Abstract: Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The effector ATR1 activates the ...Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The effector ATR1 activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of NLR RPP1. We report a cryo-electron microscopy structure of RPP1 bound by ATR1. The structure reveals a C-terminal jelly roll/Ig-like domain (C-JID) for specific ATR1 recognition. Biochemical and functional analyses show that ATR1 binds to the C-JID and the LRRs to induce an RPP1 tetrameric assembly required for nicotinamide adenine dinucleotide hydrolase (NADase) activity. RPP1 tetramerization creates two potential active sites, each formed by an asymmetric TIR homodimer. Our data define the mechanism of direct effector recognition by a plant NLR leading to formation of a signaling-active holoenzyme. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dfv.cif.gz | 409.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dfv.ent.gz | 307.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dfv_validation.pdf.gz | 754.5 KB | Display | wwPDB validaton report |
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Full document | 7dfv_full_validation.pdf.gz | 772.6 KB | Display | |
Data in XML | 7dfv_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 7dfv_validation.cif.gz | 85.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfv ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfv | HTTPS FTP |
-Related structure data
Related structure data | 30579MC 7crbC 7crcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 139009.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ZSN5 |
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-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: Tetrameric complex of RPP1 and ATR1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 409348 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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