Extended Data Fig. 7: Structural analysis of the core SnRK1 complex composed of SnRK1α2, SnRK1β2 and SnRK1βγ.

a, Convergence of the model score calculated for 15,016 good-scoring models (mean ± SD; n = 10). The scoring did not improve after the addition of more independent models. The red line depicts a lower bound on the total score. b, The sampling precision as defined by three criteria; first, the p-value calculated using the χ2- test for homogeneity of proportions (red dots); second, the effect size for the χ2-test is quantified by the Cramer’s V value (blue squares); third, sufficiently large clusters (containing at least ten models) visualized as green triangles. The vertical dotted gray line indicates the root mean square displacement (RMSD) clustering threshold at which three criteria are satisfied (p-value > 0.05, Cramer’s V < 0.10, and the population of clustered models > 0.80). The sampling precision is thus 25 Å. c, Good-scoring models were split into two populations. Using the sampling precision 25 Å as the threshold, populations of samples 1 (light red) and 2 (blue) form four clusters. 82% of the models belong to cluster 1, which has a precision of 20 Å. d, Localization density maps for sample 1 and sample 2 of cluster 1, visualized here at a threshold equal to one-tenth of the maximum. The cross-correlation of the localization density maps of the two samples is 0.958, indicating that the position of SnRK1 subunits in the two samples is effectively identical at the model precision of 20 Å. e, Structure of the core SnRK1 complex as obtained by the integrative modeling approach. The structure presents a multiscale centroid structure, that is the structure with the minimal sum of root mean square deviations from all the good-scoring models in the dominant cluster 1. f, Input cross-links (gray dashed lines) mapped on the centroid structure. g, SnRK1 domains mapped on the centroid structure. CBM, carbohydrate-binding module; α-CTD, C-terminal domain of SnRK1α2; β-CTD, C-terminal domain of SnRK1β2; CBS, cystathionine-synthetase motif; KD, kinase domain. h, Distance distribution of obtained chemical cross-links in the centroid structure. The dotted red line represents the threshold for the consistent cross-links. i, The residue contact frequency map, calculated over ten best-scoring models, is depicted by colors ranging from white (0, low frequency) to blue (1, high frequency). A contact between a pair of amino acid residues is defined by the distance between bead surfaces below 35 Å. Cross-links are plotted as green dots (consistent cross-links - XLs) or orange dots (inconsistent XLs).