Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15.

Area of Science:

• Virology
• Structural Biology
• Immunology

Background:

• SARS-CoV-2 non-structural protein 15 (Nsp15) is essential for viral replication and immune evasion.
• Nsp15's uridine-specific endoribonuclease activity cleaves the poly(U) tract in viral RNA, reducing dsRNA formation and interferon signaling.
• The precise mechanism of Nsp15's poly(U) tract recognition and cleavage remained unclear.

Approach:

• Cryogenic electron microscopy (cryo-EM) was used to determine the structures of SARS-CoV-2 Nsp15 bound to viral replication intermediate dsRNA.
• Structures were resolved at 2.7-3.3 Å resolution, capturing Nsp15 in complex with dsRNA containing a poly(U) tract.
• The binding modes and interactions within the Nsp15-dsRNA complex were analyzed.

Key Points:

• A single dsRNA molecule binds to the Nsp15 homohexamer, interacting with three subunits in two distinct states.
• Key residues (W332 and M330) dislodge uracil from dsRNA base-pairing, facilitating its entrapment in the active site.
• The hexamer anchors up to 20 A/U base pairs, explaining the shorter poly(U) sequences in negative-strand viral RNA.

Conclusions:

• The study provides high-resolution structural insights into the molecular basis of Nsp15's poly(U) tract recognition and cleavage.
• These findings elucidate a key mechanism of immune evasion employed by coronaviruses.
• The results offer a mechanistic understanding of how Nsp15 modulates host antiviral responses.