Fig. 3: Blockage of the AUD oligomerization interfaces in the non-cleaved nsP3 polyprotein.

a Superposition of the Alphafold2 predicted structure of the uncleaved nsP2-3 on the nsP3 HSs. One turn of the helical scaffold is shown in dark and light gray cartoon (for hA and hB respectively). The model is superposed in the hA AUD of the helix. It is shown with nsP2 protease surface colored in magenta, the MTase domain in olive green, the nsP3 MD domain in blue and the AUD in green cartoons. The protease domain completely blocks the axial contacts of the helical scaffold in the nsP2-3 uncleaved protein structure. b Same structure than in (a), showing only the protease domain and the AUD domain. On the left panel the residues mediating axial interactions shown in Fig. 1g are shown in spheres and colored according to panel a. On the right panel we have the same representation for the lateral contacts. The residues mutated in the replicon experiments (Y200A, P247A/V248A and K302A) are colored in red and labeled (see section “Mutations on the nsP3 AUD oligomerization interfaces affect RNA synthesis and production of structural proteins”). Only the Y200A is in the interface between the nsP2 protease and the AUD. The N terminus of the AUD connecting with the macrodomain is colored in blue.