4CO6 | pdb_00004co6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.259 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4CO6

This is version 1.3 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: https://doi.org/10.1038/nsmb.2868
  • Primary Citation Related Structures: 
    4CO6

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 139.79 kDa 
  • Atom Count: 7,650 
  • Modeled Residue Count: 970 
  • Deposited Residue Count: 1,224 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NUCLEOPROTEIN
A, B, C
356Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IK92 (Nipah virus)
Explore Q9IK92 
Go to UniProtKB:  Q9IK92
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IK92
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHOPROTEIN
D, E, F
52Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IK91 (Nipah virus)
Explore Q9IK91 
Go to UniProtKB:  Q9IK91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IK91
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR

Query on BR



Download:Ideal Coordinates CCD File
K [auth A],
O [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth B],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 2.50 Å
  • R-Value Free:  0.259 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.89α = 90
b = 98.96β = 90
c = 156.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary