4UC9

N-terminal globular domain of the RSV Nucleoprotein in complex with C- terminal dipeptide of the Phosphoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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:  
    4UCA, 4UC6, 4UC7, 4UC8, 4UC9, 4UCB, 4UCC, 4UCD, 4UCE

  • 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. This includes the recognition of its template, the ribonucleoprotein complex (RNP), consisting of genomic RNA encapsidated by the RSV nucleoprotein, N ...

    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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOPROTEINA, B, C, D233Human respiratory syncytial virus A2Mutation(s): 0 
Gene Names: N
UniProt
Find proteins for P03418 (Human respiratory syncytial virus A (strain A2))
Explore P03418 
Go to UniProtKB:  P03418
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download Ideal Coordinates CCD File 
G [auth A], K [auth B], P [auth C], S [auth D]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
ASP
Query on ASP

Download Ideal Coordinates CCD File 
F [auth A], J [auth B], O [auth C], R [auth D]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], I [auth B], L [auth C], M [auth C], N [auth C], Q [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.51α = 90
b = 72.51β = 90
c = 383.38γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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