4CO6

Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.498 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Nipah Virus Unassembled Nucleoprotein in Complex with its Viral Chaperone.

Yabukarksi, F.Lawrence, P.Tarbouriech, N.Bourhis, J.M.Delaforge, E.Jensen, M.R.Ruigrok, R.W.H.Blackledge, M.Volchkov, V.Jamin, M.

(2014) Nat.Struct.Mol.Biol. 21: 754

  • DOI: 10.1038/nsmb.2868

  • PubMed Abstract: 
  • Nipah virus (NiV) is a highly pathogenic emergent paramyxovirus causing deadly encephalitis in humans. Its replication requires a constant supply of unassembled nucleoprotein (N(0)) in complex with its viral chaperone, the phosphoprotein (P). To eluc ...

    Nipah virus (NiV) is a highly pathogenic emergent paramyxovirus causing deadly encephalitis in humans. Its replication requires a constant supply of unassembled nucleoprotein (N(0)) in complex with its viral chaperone, the phosphoprotein (P). To elucidate the chaperone function of P, we reconstituted NiV the N(0)-P core complex and determined its crystal structure. The binding of the N-terminal region of P blocks the polymerization of N by interfering with subdomain exchange between N protomers and keeps N(0) in an open conformation, ready to grasp an RNA molecule. We found that a peptide derived from the N-binding region of P protects cells against viral infection and demonstrated by structure-based mutagenesis that this peptide acts by inhibiting N(0)-P formation. These results provide new insights about the assembly of N along genomic RNA and validate the N(0)-P complex as a target for drug development.


    Organizational Affiliation

    1] Université Grenoble Alpes, Unit of Virus Host Cell Interactions, Grenoble, France. [2] CNRS, Unit of Virus Host Cell Interactions, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPROTEIN
A, B, C
356Nipah virusMutation(s): 0 
Gene Names: N
Find proteins for Q9IK92 (Nipah virus)
Go to UniProtKB:  Q9IK92
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOPROTEIN
D, E, F
52Nipah virusMutation(s): 0 
Gene Names: P/V/C
Find proteins for Q9IK91 (Nipah virus)
Go to UniProtKB:  Q9IK91
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, C
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.498 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.890α = 90.00
b = 98.960β = 90.00
c = 156.910γ = 90.00
Software Package:
Software NamePurpose
HKL2MAPphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references
  • Version 1.2: 2014-09-17
    Type: Database references