Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

Dhurvas Chandrasekaran Dinesh; Dominika Chalupska; Jan Silhan; Vaclav Veverka; Evzen Boura

Here, we report the NMR structure of the SARS-CoV-2 nucleocapsid phosphoprotein N-terminal RNA binding domain N-NTD. The structure revealed an overall right hand-like fold composed of a β-sheet core with an extended central loop. The core region adopts a five-stranded U-shaped right-handed antiparallel β-sheet platform with the topology β4-β2-β3-β1-β5 flanked by two short α-helices (α1 occurs before the β2 strand and α2 after the β4 strand). A prominent feature of the structure is a large protruding loop between β2-β3 that forms a long basic β-hairpin (β2' and β3') ( Figure 2 ). This long β-hairpin is reminiscent of a finger and composed mostly of basic amino acids residues, and we therefore refer to it as a basic finger ( Figure 2 ). This basic finger extends from the β-core structure that we refer to as a palm. Analysis of the electrostatic potential of the N-NTD revealed a highly positively charged cleft between the basic finger and the palm creating a putative RNA binding site in the hinge/junction region between the palm and basic finger. Our NMR analysis is consistent with recent X-ray analysis (PDB IDs: 6M3M and 6VYO). In addition, the NMR structure revealed that the basic finger is highly flexible (Figure 2A ) whereas in the crystal structures it is locked in one place by crystal lattice contacts.