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

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

The structural calculation was carried out in Cyana (11) using NOESY data in combination with backbone torsion angle restraints, generated from assigned chemical shifts using the program TALOS+ (12) . First, the combined automated NOE assignment and structure determination protocol (CANDID) was used for automatic NOE cross-peak assignment. Subsequently, five cycles of simulated annealing combined with redundant dihedral angle restraints were used to calculate a set of converged structures with no significant restraint violations (distance and van der Waals violations <0.5Å and dihedral angle constraint violations <5°). The 40 structures with the least restraint violations were further refined in explicit solvent using the YASARA software with the YASARA forcefield(13) and subjected to further analysis using the Protein Structure Validation Software suite (www.nesg.org). The statistics for the resulting structure is summarized in Table 1 . The structures, NMR restraints and resonance assignments were deposited in the Protein Data Bank (PDB, accession code: 6YI3) and BMRB (accession code: 34511).