6J6I

Reconstitution and structure of a plant NLR resistosome conferring immunity

• PDB DOI:  https://doi.org/10.2210/pdb6J6I/pdb
• EM Map EMD-0688: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2019-01-15 Released: 2019-03-20 
• Deposition Author(s): Wang, J.Z., Wang, J., Hu, M.J., Wang, H.W., Zhou, J.M., Chai, J.J.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Reconstitution and structure of a plant NLR resistosome conferring immunity.

Wang, J., Hu, M., Wang, J., Qi, J., Han, Z., Wang, G., Qi, Y., Wang, H.W., Zhou, J.M., Chai, J.

(2019) Science 364

• PubMed: 30948527 
• DOI: https://doi.org/10.1126/science.aav5870
• Primary Citation of Related Structures:  
  6J5T, 6J6I


• PubMed Abstract: 
  

Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. Biochemical mechanisms underlying plant NLR activation have until now remained poorly understood. We reconstituted an active complex containing the Arabidopsis coiled-coil NLR ZAR1, the pseudokinase RKS1, uridylated protein kinase PBL2, and 2'-deoxyadenosine 5'-triphosphate (dATP), demonstrating the oligomerization of the complex during immune activation. The cryo-electron microscopy structure reveals a wheel-like pentameric ZAR1 resistosome. Besides the nucleotide-binding domain, the coiled-coil domain of ZAR1 also contributes to resistosome pentamerization by forming an α-helical barrel that interacts with the leucine-rich repeat and winged-helix domains. Structural remodeling and fold switching during activation release the very N-terminal amphipathic α helix of ZAR1 to form a funnel-shaped structure that is required for the plasma membrane association, cell death triggering, and disease resistance, offering clues to the biochemical function of a plant resistosome.

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Organizational Affiliation: 

Institute of Biochemistry, University of Cologne, Zuelpicher Strasse 47, 50674 Cologne, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A5B1C1 Local Symmetry: Cyclic - C5  (3D View)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (3D View)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 575.42 kDa 
• Atom Count: 35,991 
• Modelled Residue Count: 4,472 
• Deposited Residue Count: 5,037 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable serine/threonine-protein kinase PBL2	A	426	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PBL2, APK2A, KIN1, At1g14370, F14L17.14 EC: 2.7.11.1
UniProt
Find proteins for O49839 (Arabidopsis thaliana) Explore O49839  Go to UniProtKB:  O49839

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase superfamily protein	B	351	Arabidopsis thaliana	Mutation(s): 0  Gene Names: F15B8.100, Resistance related KinaSe 1, RKS1, At3g57710, ZRK1, QRX3 EC: 2.7.11.1
UniProt
Find proteins for Q9SVY5 (Arabidopsis thaliana) Explore Q9SVY5  Go to UniProtKB:  Q9SVY5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance RPP13-like protein 4	C, D [auth F], E [auth G], F [auth L], G [auth O]	852	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RPP13L4, ZAR1, At3g50950, F18B3.230
UniProt
Find proteins for Q38834 (Arabidopsis thaliana) Explore Q38834  Go to UniProtKB:  Q38834

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP	J [auth C], K [auth F], L [auth G], M [auth L], N [auth O]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
U5P	H [auth A], I [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Wang, J.Z., Wang, J., Hu, M.J., Wang, H.W., Zhou, J.M., Chai, J.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31421001
National Natural Science Foundation of China	China	31420103906

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2023-04-12
  Changes: Advisory, Atomic model, Data collection, Data processing, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary