4UC7

N-terminal globular domain of the RSV Nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Druggable Pocket at the Nucleocapsid/Phosphoprotein Interaction Site of the Human Respiratory Syncytial Virus.

Ouizougun-Oubari, M.Pereira, N.Tarus, B.Galloux, M.Lassoued, S.Fix, J.Tortorici, M.A.Hoos, S.Baron, B.England, P.Desmaele, D.Couvreur, P.Bontems, F.Rey, F.A.Eleouet, J.F.Sizun, C.Slama-Schwok, A.Duquerroy, S.

(2015) J.Virol. 89: 11129

  • DOI: 10.1128/JVI.01612-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Presently, respiratory syncytial virus (RSV), the main cause of severe respiratory infections in infants, cannot be treated efficiently with antivirals. However, its RNA-dependent polymerase complex offers potential targets for RSV-specific drugs. Th ...

    Presently, respiratory syncytial virus (RSV), the main cause of severe respiratory infections in infants, cannot be treated efficiently with antivirals. However, its RNA-dependent polymerase complex offers potential targets for RSV-specific drugs. This includes the recognition of its template, the ribonucleoprotein complex (RNP), consisting of genomic RNA encapsidated by the RSV nucleoprotein, N. This recognition proceeds via interaction between the phosphoprotein P, which is the main polymerase cofactor, and N. The determinant role of the C terminus of P, and more particularly of the last residue, F241, in RNP binding and viral RNA synthesis has been assessed previously. Here, we provide detailed structural insight into this crucial interaction for RSV polymerase activity. We solved the crystallographic structures of complexes between the N-terminal domain of N (N-NTD) and C-terminal peptides of P and characterized binding by biophysical approaches. Our results provide a rationale for the pivotal role of F241, which inserts into a well-defined N-NTD pocket. This primary binding site is completed by transient contacts with upstream P residues outside the pocket. Based on the structural information of the N-NTD:P complex, we identified inhibitors of this interaction, selected by in silico screening of small compounds, that efficiently bind to N and compete with P in vitro. One of the compounds displayed inhibitory activity on RSV replication, thereby strengthening the relevance of N-NTD for structure-based design of RSV-specific antivirals.


    Organizational Affiliation

    Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France.,UMR CNRS 8612, Institut Galien Paris-Sud, Châtenay-Malabry, France.,Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France sduquer@pasteur.fr christina.sizun@cnrs.fr.,Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, Paris, France CNRS UMR 3569 Virologie, Paris, France.,Institut Pasteur, Protéopôle, CNRS UMR 3528, Paris, France.,Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Jouy-en-Josas, France.,Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, Paris, France CNRS UMR 3569 Virologie, Paris, France Université Paris-Sud, Faculté des Sciences, Orsay, France sduquer@pasteur.fr christina.sizun@cnrs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
A
233Human respiratory syncytial virus A (strain A2)Mutation(s): 0 
Gene Names: N
Find proteins for P03418 (Human respiratory syncytial virus A (strain A2))
Go to UniProtKB:  P03418
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
B
233Human respiratory syncytial virus A (strain A2)Mutation(s): 0 
Gene Names: N
Find proteins for P03418 (Human respiratory syncytial virus A (strain A2))
Go to UniProtKB:  P03418
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.310α = 90.00
b = 72.130β = 90.00
c = 181.670γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references