Extended Data Fig. 6: The AlphaFold2 multimer model predictions and fitting to the RS3 head-neck region.

a–d) Each row shows a complex prediction between of two RS3 proteins as labelled and colored in the second column, that is two catalytic domains of AK9 with LRRC23s (a, b), the C-terminal fragments of AK7 and AK9 (c), and the C-terminal fragment of AK9 with the N-terminal fragment of MDH1B (d). The first column shows the AlphaFold2 multimer model predictions^103,104 color-coded by ‘per-residue confidence score’ (pLDDT) from the highest (blue) to the lowest score (red). Note that the confidence scores are mostly high at the predicted protein interfaces. The second and third columns show the predicted AlphaFold2 multimer model fitted into our cryo-EM map without (2^nd column) and with refinement (3^rd column); note that other RS3 proteins are not shown in the cryo-EM map for clarity; black arrowheads highlight some of the larger refinements. Detailed fitting and refinement of the individual residues into the density was carried out with secondary structure restraints, and was further refined for coordinates and b-factor with secondary structure and Ramachandran restraints¹⁰⁶. The fourth column shows a zoomed-out overview with the region shown in the third column indicated by a box. a’-d’) Predicted aligned error (PAE) plot showing low (blue) to high (red) alignment error between chains for the corresponding predictions in panels a-d.

Source data