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- PDB-7crb: Cryo-EM structure of plant NLR RPP1 LRR-ID domain in complex with ATR1 -

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Basic information

Entry
Database: PDB / ID: 7crb
TitleCryo-EM structure of plant NLR RPP1 LRR-ID domain in complex with ATR1
Components
  • Avirulence protein ATR1
  • NAD+ hydrolase (NADase)
KeywordsPLANT PROTEIN / NADase / ETI / HR
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
: / Avirulence protein ATR1, WY-domain / Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...: / Avirulence protein ATR1, WY-domain / Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Avirulence protein ATR1 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesHyaloperonospora arabidopsidis (eukaryote)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsMa, 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
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31421001 to J.C. China
Alexander von Humboldt Foundationa Humboldt professorship to J.C. Germany
CitationJournal: 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
DepositionAug 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • EMDB-30449
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Assembly

Deposited unit
J: Avirulence protein ATR1
A: NAD+ hydrolase (NADase)


Theoretical massNumber of molelcules
Total (without water)174,1592
Polymers174,1592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Avirulence protein ATR1 / Arabidopsis thaliana recognized protein 1


Mass: 35149.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyaloperonospora arabidopsidis (strain Emoy2) (eukaryote)
Gene: ATR1, ATR1-NdWsB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: M4B6G6
#2: Protein NAD+ hydrolase (NADase) / RPP1 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase


Mass: 139009.781 Da / Num. of mol.: 1
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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1local structure of RPP1 LRR-ID domain bound with ATR1COMPLEXall0RECOMBINANT
2ATR1COMPLEX#11RECOMBINANT
3RPP1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Hyaloperonospora arabidopsidis (strain Emoy2) (eukaryote)559515
23Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 23.542 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222015 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056946
ELECTRON MICROSCOPYf_angle_d0.6689413
ELECTRON MICROSCOPYf_dihedral_angle_d15.489918
ELECTRON MICROSCOPYf_chiral_restr0.0451088
ELECTRON MICROSCOPYf_plane_restr0.0031199

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