7DFV | pdb_00007dfv

Cryo-EM structure of plant NLR RPP1 tetramer core part

• PDB DOI: https://doi.org/10.2210/pdb7DFV/pdb
• EM Map EMD-30579: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-11-10 Released: 2020-12-16 
• Deposition Author(s): 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 Organization(s): National Natural Science Foundation of China (NSFC), Alexander von Humboldt Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme.

Ma, S., Lapin, D., Liu, L., Sun, Y., Song, W., Zhang, X., Logemann, E., Yu, D., Wang, J., Jirschitzka, J., Han, Z., Schulze-Lefert, P., Parker, J.E., Chai, J.

(2020) Science 370

• PubMed: 33273071 
• DOI: https://doi.org/10.1126/science.abe3069
• Primary Citation Related Structures: 
  7CRB, 7CRC, 7DFV


• PubMed Abstract: 
  

  Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The Hyaloperonospora arabidopsidis effector ATR1 activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis 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.

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Organizational Affiliation: 
• Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.
Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany.
Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. [e-mail] [e-mail] [e-mail].
Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 556.04 kDa 
• Atom Count: 16,580 
• Modeled Residue Count: 2,072 
• Deposited Residue Count: 4,884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD+ hydrolase (NADase)	A [auth B], B [auth C], C [auth D], D [auth A]	1,221	Arabidopsis thaliana	Mutation(s): 0  EC: 3.2.2.6
UniProt
Find proteins for Q9ZSN5 (Arabidopsis thaliana) Explore Q9ZSN5  Go to UniProtKB:  Q9ZSN5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31421001 for J.C.
Alexander von Humboldt Foundation	Germany	--

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary