6LZ8

Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation.

Hsu, J.N.Chen, J.S.Lin, S.M.Hong, J.Y.Chen, Y.J.Jeng, U.S.Luo, S.Y.Hou, M.H.

(2022) Front Mol Biosci 9: 871499-871499

  • DOI: https://doi.org/10.3389/fmolb.2022.871499
  • Primary Citation of Related Structures:  
    6LNN, 6LZ6, 6LZ8, 7DYD

  • PubMed Abstract: 

    Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs.


  • Organizational Affiliation

    Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NucleoproteinA,
B [auth C],
C [auth B],
D
130Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for K9N4V7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N4V7 
Go to UniProtKB:  K9N4V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N4V7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EY9 (Subject of Investigation/LOI)
Query on EY9

Download Ideal Coordinates CCD File 
E [auth D]5-(2-methoxyethoxy)-1H-indole
C11 H13 N O2
FPLAYGBHGUOPLD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.154α = 90
b = 111.028β = 100.97
c = 92.261γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description