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- PDB-7dfv: Cryo-EM structure of plant NLR RPP1 tetramer core part -

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Basic information

Entry
Database: PDB / ID: 7dfv
TitleCryo-EM structure of plant NLR RPP1 tetramer core part
ComponentsNAD+ hydrolase (NADase)
KeywordsPLANT PROTEIN / NADase / ETI / HR
Function / homology
Function and homology information


ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / defense response / ADP binding / signal transduction
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain ...Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein Roq1-like, winged-helix 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
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 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 for J.C. China
Alexander von Humboldt Foundation 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
DepositionNov 10, 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
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Assembly

Deposited unit
B: NAD+ hydrolase (NADase)
C: NAD+ hydrolase (NADase)
D: NAD+ hydrolase (NADase)
A: NAD+ hydrolase (NADase)


Theoretical massNumber of molelcules
Total (without water)556,0394
Polymers556,0394
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
NAD+ hydrolase (NADase) / RPP1


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
Has protein modificationN

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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

ComponentName: Tetrameric complex of RPP1 and ATR1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 409348 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616898
ELECTRON MICROSCOPYf_angle_d0.69322736
ELECTRON MICROSCOPYf_dihedral_angle_d17.8542228
ELECTRON MICROSCOPYf_chiral_restr0.0482502
ELECTRON MICROSCOPYf_plane_restr0.0042908

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