9RIA | pdb_00009ria

Cryo-EM structure of tomato NRC3-AVRcap1b complex

• PDB DOI: https://doi.org/10.2210/pdb9RIA/pdb
• EM Map EMD-53991: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Solanum lycopersicum, Phytophthora infestans
• 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), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of tomato NRC3-AVRcap1b complex

Seager, B.A., Kamoun, S., Madhuprakash, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 393.95 kDa 
• Atom Count: 24,721 
• Modeled Residue Count: 3,075 
• Deposited Residue Count: 3,441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SlNRC3	A, B, C	919	Solanum lycopersicum	Mutation(s): 3  Gene Names: LOC101260638
UniProt
Find proteins for A0A3Q7GDL1 (Solanum lycopersicum) Explore A0A3Q7GDL1  Go to UniProtKB:  A0A3Q7GDL1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein PITG_16705	D [auth G]	684	Phytophthora infestans	Mutation(s): 1  Gene Names: PITG_16705
UniProt
Find proteins for D0NVF3 (Phytophthora infestans (strain T30-4)) Explore D0NVF3  Go to UniProtKB:  D0NVF3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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/V002937/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/Y002997/1
European Research Council (ERC)	European Union	EP/Y032187/1

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release