6KL2

Structure of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure-Based Stabilization of Non-native Protein-Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design.

Lin, S.M., Lin, S.C., Hsu, J.N., Chang, C.K., Chien, C.M., Wang, Y.S., Wu, H.Y., Jeng, U.S., Kehn-Hall, K., Hou, M.H.

(2020) J Med Chem 63: 3131-3141

  • DOI: 10.1021/acs.jmedchem.9b01913
  • Primary Citation of Related Structures:  
    6KL2, 6KL6, 6KL5

  • PubMed Abstract: 

    • Structure-based stabilization of protein-protein interactions (PPIs) is a promising strategy for drug discovery. However, this approach has mainly focused on the stabilization of native PPIs, and non-native PPIs have received little consideration. He ...

    Structure-based stabilization of protein-protein interactions (PPIs) is a promising strategy for drug discovery. However, this approach has mainly focused on the stabilization of native PPIs, and non-native PPIs have received little consideration. Here, we identified a non-native interaction interface on the three-dimensional dimeric structure of the N-terminal domain of the MERS-CoV nucleocapsid protein (MERS-CoV N-NTD). The interface formed a conserved hydrophobic cavity suitable for targeted drug screening. By considering the hydrophobic complementarity during the virtual screening step, we identified 5-benzyloxygramine as a new N protein PPI orthosteric stabilizer that exhibits both antiviral and N-NTD protein-stabilizing activities. X-ray crystallography and small-angle X-ray scattering showed that 5-benzyloxygramine stabilizes the N-NTD dimers through simultaneous hydrophobic interactions with both partners, resulting in abnormal N protein oligomerization that was further confirmed in the cell. This unique approach based on the identification and stabilization of non-native PPIs of N protein could be applied toward drug discovery against CoV diseases.

    Organizational Affiliation: 

    Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinA, B, C, D144Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Find proteins for K9N4V7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N4V7 
Go to UniProtKB:  K9N4V7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.601α = 90
b = 109.645β = 101.23
c = 91.993γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references