9RI9 | pdb_00009ri9

Cryo-EM structure of the tomato NRC3 hexameric resistosome

• PDB DOI: https://doi.org/10.2210/pdb9RI9/pdb
• EM Map EMD-53990: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Solanum lycopersicum
• Expression System: Nicotiana benthamiana
• Mutation(s): Yes 


• Deposited: 2025-06-11 Released: 2025-07-23 
• Deposition Author(s): Seager, B.A., Kamoun, S., Madhuprakash, J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Gatsby Charitable Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A plant pathogen effector blocks stepwise assembly of a helper NLR resistosome

Seager, B.A., Harant, A., Contreras, M.P., Hou, L.Y., Wu, C.H., Kamoun, S., Madhuprakash, J.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.07.14.664264

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 631.63 kDa 
• Atom Count: 41,886 
• Modeled Residue Count: 5,208 
• Deposited Residue Count: 5,514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRC3	A [auth B], B [auth D], C [auth G], D [auth I], E [auth J], F [auth L]	919	Solanum lycopersicum	Mutation(s): 3  Gene Names: LOC101260638
UniProt
Find proteins for A0A3Q7GDL1 (Solanum lycopersicum) Explore A0A3Q7GDL1  Go to UniProtKB:  A0A3Q7GDL1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	G [auth B], H [auth D], I [auth G], J [auth I], K [auth J], L	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.21.2
MODEL REFINEMENT	ISOLDE	1.8

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Seager, B.A., Kamoun, S., Madhuprakash, J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/Y002997/1
Gatsby Charitable Foundation	United Kingdom	--
European Research Council (ERC)	European Union	EP/Y032187/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V002937/1

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 1.1: 2026-02-04
  Changes: Data collection, Database references, Structure summary