3PMK | pdb_00003pmk

Crystal structure of the Vesicular Stomatitis Virus RNA free nucleoprotein/phosphoprotein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 
    0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of the Vesicular Stomatitis Virus N0-P Complex

Leyrat, C.Yabukarski, F.Tarbouriech, N.Ribeiro, E.A.Jensen, M.R.Blackledge, M.Ruigrok, R.W.Jamin, M.

(2011) PLoS Pathog 7: e1002248-e1002248

  • DOI: https://doi.org/10.1371/journal.ppat.1002248
  • Primary Citation Related Structures: 
    3PMK

  • PubMed Abstract: 

    Replication of non-segmented negative-strand RNA viruses requires the continuous supply of the nucleoprotein (N) in the form of a complex with the phosphoprotein (P). Here, we present the structural characterization of a soluble, heterodimeric complex between a variant of vesicular stomatitis virus N lacking its 21 N-terminal residues (N(Δ21)) and a peptide of 60 amino acids (P(60)) encompassing the molecular recognition element (MoRE) of P that binds RNA-free N (N(0)). The complex crystallized in a decameric circular form, which was solved at 3.0 Å resolution, reveals how the MoRE folds upon binding to N and competes with RNA binding and N polymerization. Small-angle X-ray scattering experiment and NMR spectroscopy on the soluble complex confirms the binding of the MoRE and indicates that its flanking regions remain flexible in the complex. The structure of this complex also suggests a mechanism for the initiation of viral RNA synthesis.


  • Organizational Affiliation
    • UMI 3265 UJF-EMBL-CNRS Unit of Virus Host Cell Interactions, Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 267.49 kDa 
  • Atom Count: 17,478 
  • Modeled Residue Count: 2,167 
  • Deposited Residue Count: 2,360 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleocapsid protein
A, B, C, D, E
404Recombinant vesicular stomatitis Indiana virus rVSV-G/GFPMutation(s): 0 
Gene Names: NNucleoprotein
UniProt
Find proteins for B7UCZ2 (Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP)
Explore B7UCZ2 
Go to UniProtKB:  B7UCZ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7UCZ2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PhosphoproteinF [auth N],
G [auth O],
H [auth P],
I [auth Q],
J [auth R]
68Recombinant vesicular stomatitis Indiana virus rVSV-G/GFPMutation(s): 0 
Gene Names: PPhosphoprotein
UniProt
Find proteins for B7UCZ3 (Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP)
Explore B7UCZ3 
Go to UniProtKB:  B7UCZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7UCZ3
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free:  0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.56α = 90
b = 171.97β = 90
c = 239.86γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description