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)

---

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.

(2026) Sci Adv 12: eaeb1931-eaeb1931

• PubMed: 42247517 
• DOI: https://doi.org/10.1126/sciadv.aeb1931
• Primary Citation Related Structures: 
  9RI9, 9RIA


• PubMed Abstract: 
  

  Helper NLRs function as central nodes in plant immune networks. Upon activation, they oligomerize into inflammasome-like resistosomes to initiate immune signaling, yet the dynamics of resistosome assembly remain poorly understood. Here, we show that the virulence effector AVRcap1b from the Irish potato famine pathogen Phytophthora infestans suppresses immune activation by directly engaging oligomerization intermediates of the tomato helper NLR SlNRC3. Cryo-EM structures of SlNRC3 in AVRcap1b-bound and unbound states reveal that AVRcap1b bridges multiple protomers, stabilizing a stalled intermediate and preventing formation of a functional resistosome. Leveraging AVRcap1b as a molecular tool, we also capture an additional SlNRC3 resistosome intermediate showing that assembly proceeds in a stepwise manner from dissociated monomers. These findings uncover a previously unrecognized vulnerability in NLR activation and reveal a pathogen strategy that disrupts immune complex assembly. This work advances mechanistic understanding of resistosome formation and uncovers a previously unrecognized facet of pathogen-plant coevolution.

---

Organizational Affiliation: 
• The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India.

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.

---

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
• Version 1.2: 2026-06-17
  Changes: Data collection, Database references