Journal Article

A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding

Becker, Matthias A., Günther, Sebastian, Schwalbe, Harald, Dhamotharan, Karthikeyan, Schlundt, Andreas, Korn, Sophie M., Wacker, Anna

2024

Overview

The SARS-CoV-2 nucleocapsid protein is indispensable for viral RNA genome processing. Although the N-terminal domain (NTD) is suggested to mediate specific RNA-interactions, high-resolution structures with viral RNA are still lacking. Available hybrid structures of the NTD with ssRNA and dsRNA provide valuable insights; however, the precise mechanism of complex formation remains elusive. Similarly, the molecular impact of nucleocapsid NTD mutations that have emerged since 2019 has not yet been fully explored. Using crystallography and solution NMR, we investigate how NTD mutations influence structural integrity and RNA-binding. We find that both features rely on a core network of residues conserved in Betacoronaviruses , crucial for protein stability and communication among flexible loop-regions that facilitate RNA-recognition. Our comprehensive structural analysis demonstrates that contacts within this network guide selective RNA-interactions. We propose that the core network renders the NTD evolutionarily robust in stability and plasticity for its versatile RNA processing roles. The authors use solution-state NMR and X-ray crystallography to study mutations in the SARS-CoV-2 Nucleocapsid NTD, uncovering a network essential for protein integrity and the selectively of RNA binding.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/6 / 631/45/535/878/1263 / 631/45/612/1230 / 631/535/1266 / 82/83 / Binding / Binding Sites / Complex formation / Coronavirus Nucleocapsid Proteins - chemistry / Coronavirus Nucleocapsid Proteins - genetics / Coronavirus Nucleocapsid Proteins - metabolism / COVID-19 / COVID-19 - virology / Crystallography / Crystallography, X-Ray / Double-stranded RNA / Humanities and Social Sciences / Humans / Hybrid structures / Magnetic Resonance Spectroscopy / Models, Molecular / multidisciplinary / Mutation / NMR / Nuclear magnetic resonance / Nucleocapsid - metabolism / Nucleocapsid Proteins - chemistry / Nucleocapsid Proteins - genetics / Nucleocapsid Proteins - metabolism / Nucleocapsids / Phosphoproteins - chemistry / Phosphoproteins - genetics / Phosphoproteins - metabolism / Protein Binding / Protein Domains / Proteins / RNA processing / RNA, Viral - chemistry / RNA, Viral - genetics / RNA, Viral - metabolism / SARS-CoV-2 - genetics / SARS-CoV-2 - metabolism / Science / Science (multidisciplinary) / Severe acute respiratory syndrome coronavirus 2 / Structural analysis / Structural integrity / X-ray crystallography