+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30451 | |||||||||
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Title | Cryo-EM map of RPP1 mutant in complex with ATR1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information effector-mediated modulation of host process by symbiont / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / ADP binding / defense response / host cell cytoplasm / host cell nucleus / signal transduction / extracellular region Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / Hyaloperonospora arabidopsidis Emoy2 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||
Authors | Ma SC / Lapin D / Liu L / Sun Y / Song W / Zhang XX / Logemann E / Yu DL / Wang J / Jirschitzka J ...Ma SC / Lapin D / Liu L / Sun Y / Song W / Zhang XX / Logemann E / Yu DL / Wang J / Jirschitzka J / Han ZF / SchulzeLefert P / Parker JE / Chai JJ | |||||||||
Funding support | China, Germany, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30451.map.gz | 124.2 MB | EMDB map data format | |
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Header (meta data) | emd-30451-v30.xml emd-30451.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_30451.png | 40.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30451 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30451.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tetrameric complex of RPP1 and ATR1
Entire | Name: Tetrameric complex of RPP1 and ATR1 |
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Components |
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-Supramolecule #1: Tetrameric complex of RPP1 and ATR1
Supramolecule | Name: Tetrameric complex of RPP1 and ATR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: RPP1
Supramolecule | Name: RPP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Supramolecule #3: ATR1
Supramolecule | Name: ATR1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Hyaloperonospora arabidopsidis Emoy2 (eukaryote) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 23.542 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178011 |