Figure 4. SARS-CoV-2 nsp12-NiRAN domain, pseudokinase SelO, and ADP binding.

a. The colored histograms denote identity in a sequence alignment of 45 α- and β-CoV nsp12 sequences (red bar, 100% identity; dark blue bar, ≤ 20%) in the N-terminal signature motifs A_N, B_N, and C_N (Lehmann et al., 2015) of the NiRAN domain. The consensus sequence is shown just below. The SARS-CoV-2 nsp12 and the pseudokinase P. syringae (Psy) SelO (Sreelatha et al., 2018) are aligned below. Residues that are 100% identical in the nsp12 alignment and conserved in SelO are highlighted by a red dot underneath.

b. (left) Structures of the SARS-CoV-2 NiRAN domain (cyan ribbon) with ADP-Mg²⁺ (spheres) and Psy SelO (orange) with AMP-PNP-Mg²⁺ (6EAC; Sreelatha et al., 2018). The A_N, B_N, and C_N regions are highlighted.

(right) Structure-based alignment via α-carbons of the A_N, B_N, and C_N regions, with side chains of conserved residues shown. The α- and β-phosphates of the NiRAN-domain ADP-Mg²⁺ (limon carbon atoms, yellow sphere, respectively) superimpose almost exactly with the β- and γ-phosphates of the SelO AMP-PNP-Mg²⁺ (dark gray), whereas the nucleoside moieties diverge.

c. The ADP-Mg²⁺-bound pocket of the SARS-CoV-2 NiRAN domain is shown. Side chains interacting with the ADP-Mg²⁺ are shown (polar interactions are denoted by gray dashed lines). D208 likely makes a water-mediated interaction with the Mg²⁺ (Sreelatha et al., 2018). The cryo-EM difference density for the ADP-Mg²⁺ is shown (light gray mesh).