Nithin 6wxd
From Proteopedia
SARS-CoV-2 Main Protease (Mpro) – Structure and Covalent Inhibition
This page provides structural overview of the SARS-CoV-2 main protease (Mpro), based on the iScience 2020 study (DOI: https://doi.org/10.1016/j.isci.2020.101258) and the crystal structure 6XWD. In this study , the researchers produced SARS-CoV-2 Nsp9 in the lab and sloved its X-ray crystal structure
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Structure
The SARS-CoV-2 Nsp9 monomer adopts a compact **7-stranded β-barrel fold**, a hallmark feature of the Nsp9 family. Two monomers form a **homodimer**, which is necessary for RNA-binding function.
β-Barrel Core
The Nsp9 monomer contains **seven antiparallel β-strands** arranged into a barrel-like fold. This β-barrel provides rigidity and forms the structural foundation needed for RNA interaction. The fold is nearly identical to SARS-CoV Nsp9, highlighting strong evolutionary conservation.
Dimer Interface
Nsp9 functions as a **homodimer**. The dimer interface is primarily stabilized by:
- β5–β6 region interactions
- Hydrophobic packing
- A conserved **GxGxG motif** situated near the dimerization surface
The alignment of the two monomers creates a positively charged groove thought to accommodate viral RNA.
Peptide-Binding Site (LEVL peptide)
In the peptide-bound structure (6WXD), a short peptide (**LEVL**) occupies a groove near the dimer interface. This interaction was **not biologically intended** but arose from purification artifacts involving the rhinovirus 3C protease.
Nevertheless, the peptide influences monomer orientation, providing insight into how small ligands or interacting partners may modulate Nsp9 dimer architecture.
Key features:
- Peptide binds in a shallow hydrophobic groove
- Contacts β-barrel residues at the interface
- Causes measurable shifts in dimer alignment
- Suggests the site may be relevant for RNA or protein interactions
Conserved Motif
A highly conserved **Gly-rich GxGxG loop** is found near the dimerization surface. Evolutionary conservation suggests this motif stabilizes the fold and may contribute to RNA association. Mutations in this region in related coronaviruses reduce replication efficiency.
Biological Significance
Nsp9 is essential for:
- Assembly of the replication–transcription complex
- Stabilization of viral RNA
- Viral protein–protein interactions
- Efficient SARS-CoV-2 genome replication
The structural analysis in this paper showed:
- Nsp9’s β-barrel is rigid and conserved
- Dimerization is critical for function
- The unexpected LEVL peptide reveals a **potential regulatory pocket**
- Small ligands may modulate Nsp9 dimer dynamics
Because Nsp9 lacks close human homologs, identifying druggable sites on this protein could offer future antiviral opportunities.
References
[1] iScience (2020). Structural Basis of SARS-CoV-2 Main Protease Inhibition. https://doi.org/10.1016/j.isci.2020.101258
[2] Protein Data Bank: PDB 6WXD
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