Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9

Dene Littler; Benjamin Gully; Rhys N Colson; Jamie Rossjohn

The arrangement of monomers within Nsp9-dimers is wellconserved in different viruses and is maintained within Nsp9COV19 (R.M.S.D of 0.66Å over 226Cα compared to the dimeric unit of Nsp9SARS). The main component of the intersubunit interaction is the self-association of the conserved GxxxG protein-protein binding motif (Fig. 3C ) that allowed backbone van der Waals interactions between interfacing copies of the C-terminal α1-helix (Hu et al. 2017) . Here Gly-100 of the respective parallel α1-helices, formed complementary backbone van der Waals interactions. These interactions were replicated after a full helical turn by Gly-104 of the respective chains, thereby forming the molecular basis of the Nsp9COVID19 dimer interface (Fig. 3C) . The 2-fold axis that created the dimer ran at a ~15 ° angle through the GxxxG motif allowing the 14-residue helix to cross its counterpart (Fig. 4A ), the N-terminal turns of the helix were relatively isolated, only making contacts with counterpart protomer residues. In contrast, the Cterminal portions were encircled by hydrophobic residues, albeit at a distance that created funnel-like hydrophobic cavities either side of the interfacing helices (Fig. 3A) . Strands β1, β6 and the protein's C-terminus served to provide a ring of residues that encircled the paired helices. The first 10 residues of Nsp9COV19 exchanged across the dimer-interface to form a strand-like extension of β1 that ran alongside β6 from the other protomer (Fig. 3A) . The interaction these strands made did not appear optimal, indeed the remaining four C-terminal residues projected sideways across the dimer interface, inserting between the two strands while contributing a hydrophobic backing to the main helix.