AlphaFold 3 predicted NLR resistosome structures

Abstract

In our paper "A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity," we used the NbNRC2 hexamer structure to evaluate the capabilities of the newly introduced AlphaFold 3 in predicting activated CC-NLR oligomers. Our analysis highlights AlphaFold 3 effectiveness in confidently modelling the N-terminal alpha1-helices of NbNRC2 and other CC-NLRs, a structurally elusive region critical for NLR function but challenging to resolve through conventional structural methods. This study not only underscores the utility of AlphaFold 3 in enhancing our understanding of plant immune receptors but also extends its application to complex oligomerization processes in innate immunity. Here, we provide the Supplementary data accompanying the paper which includes metadata and predicted structures for 29 NLR immune receptors, providing valuable resources for further research in plant pathogen resistance.

Index:

Metadata:

Metadata, sequence, and model statistics of all modelled NLRs:

Data S1.xlsx

Predicted structures:

AlphaFold 2 vs 3 vs 3+lipids comparison for NbNRC2:

AF_benchmark.zip

[AlphaFold 3] NRC2 oliogmoeric type benchmarks (N = 10):

NRC2_tetramers.zip

NRC2_pentamers.zip

NRC2_hexamers.zip

NRC2_heptamers.zip

NRC2_octamers.zip

[AlphaFold 3] Pentamer vs Hexamer comparison for 11 representative NRC proteins:

NRCs.zip

[AlphaFold 3] Pnetamer vs Hexamer comparison for AtZAR1 (PDB:6j5t) and TmSr35 (PDB:7xe0) experimentally validated cryo-EM structure:

Benchmarks.zip

[AlphaFold 3] Pentamer vs Hexamer comparison for a selection of 8 CC, 6 CCG10, and 2 CCR-NLRs:

CC.zip

CCG10.zip

CCR.zip