Extended Data Fig. 2: Cryo-EM analysis of a signal-subtracted LRRK2^RCKW trimer and map-to-model fit.

a, Processing strategy used to obtain a 3.8 Å structure of LRRK2^RCKW generated from a signal-subtracted trimer where only one monomer contains the ROC and COR-A domains. This structure improved the resolution of the ROC and COR-A domains relative to the full trimer (Extended Data Fig. 1). b–d, 2D class averages (b), Fourier shell correlations (from Relion) (c), and Euler angle distribution (from Relion) (d) for the 3.8 Å resolution signal-subtracted LRRK2^RCKW structure. e, Close-ups (f–l) of different parts of the final model fit into the map. f, Section of the WD40 domain. g, C-terminal helix and its interface with the kinase domain. h, Active site of the kinase. Residues in the DYG motif are labelled. G2019, the site of a major PD-associated mutation (G2019S) and the last residue of the activation loop seen in our structure, is highlighted by a black rounded square. i, Interface between COR-B and the αC helix of the N-lobe of the kinase domain. j, Interface between the ROC and COR-B domains. R1441 and Y1699, two residues mutated in Parkinson’s disease, are labelled. k, l, Two different views of the ROC and COR-A domains with GDP-Mg²⁺ modelled into the density. Side chains were omitted in these two panels, corresponding to the lowest-resolution parts of the map. m, Map-to-model FSC plots for the top-ranked LRRK2^RCKW models, with (left) or without (right) GDP-Mg²⁺ (right) in the ROC domain. The 0.143 FSC values are reported in Supplementary Table 1. n, Size exclusion chromatography–multiple angle light scattering (SEC–MALS) analysis of LRRK2^RCKW under the conditions used for cryo-EM (Fig. 1). The table shows the calculated molecular weights (MW) of LRRK2^RCKW according to SEC standards and MALS.