4R94

Structure of the nickase domain of NS1 from MVM complexed with magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.668 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.

Tewary, S.K.Liang, L.Lin, Z.Lynn, A.Cotmore, S.F.Tattersall, P.Zhao, H.Tang, L.

(2014) Virology 476C: 61-71

  • DOI: 10.1016/j.virol.2014.11.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure ...

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins.


    Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein NS1
A
255Murine minute virus (strain MVM prototype)Mutation(s): 0 
Gene Names: NS1
EC: 3.1.21.-, 3.6.4.12
Find proteins for P03134 (Murine minute virus (strain MVM prototype))
Go to UniProtKB:  P03134
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.668 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.016α = 90.00
b = 121.377β = 90.00
c = 41.581γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description