8A4Y | pdb_00008a4y

SARS-CoV-2 non-structural protein-1 (nsp1) in complex with N-(2,3-dihydro-1H-inden-5-yl)acetamide

• PDB DOI: https://doi.org/10.2210/pdb8A4Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-13 Released: 2022-11-23 
• Deposition Author(s): Borsatto, A., Galdadas, I., Ma, S., Damfo, S., Haider, S., Kozielski, F., Estarellas, C., Gervasio, F.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.166 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other beta-coronaviruses by simulations and crystallography.

Borsatto, A., Akkad, O., Galdadas, I., Ma, S., Damfo, S., Haider, S., Kozielski, F., Estarellas, C., Gervasio, F.L.

(2022) Elife 11

• PubMed: 36412088 
• DOI: https://doi.org/10.7554/eLife.81167
• Primary Citation Related Structures: 
  8A4Y


• PubMed Abstract: 
  

  Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α - and β - coronaviruses. Nsp1 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S host ribosomal subunits and promoting host mRNA degradation. This mechanism leads to the downregulation of the translation-mediated innate immune response in host cells, ultimately mediating the observed immune evasion capabilities of SARS-CoV-2. Here, by combining extensive molecular dynamics simulations, fragment screening and crystallography, we reveal druggable pockets in Nsp1. Structural and computational solvent mapping analyses indicate the partial crypticity of these newly discovered and druggable binding sites. The results of fragment-based screening via X-ray crystallography confirm the druggability of the major pocket of Nsp1. Finally, we show how the targeting of this pocket could disrupt the Nsp1-mRNA complex and open a novel avenue to design new inhibitors for other Nsp1s present in homologous β - coronaviruses.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
ISPSO, University of Geneva, Geneva, Switzerland.
School of Pharmacy, University College London, London, United Kingdom.
UCL Centre for Advanced Research Computing, University College London, London, United Kingdom.
Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Theoretical and Computational Chemistry, University of Barcelona, Barcelona, Spain.
Chemistry Department, University College London, London, United Kingdom.
Institute of Structural and Molecular Biology, University College London, London, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.28 kDa 
• Atom Count: 1,082 
• Modeled Residue Count: 118 
• Deposited Residue Count: 118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Host translation inhibitor nsp1	A	118	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QO6 (Subject of Investigation/LOI)	B [auth A]	N-(2,3-dihydro-1H-inden-5-yl)acetamide C11 H13 N O WOYOJAPRKMBKEU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.166 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.688	α = 90
b = 36.688	β = 90
c = 140.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Borsatto, A., Galdadas, I., Ma, S., Damfo, S., Haider, S., Kozielski, F., Estarellas, C., Gervasio, F.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description