7SZY

High-resolution structure of the nuclease domain from the main replication protein NS1 of Human Parvovirus B19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1.

Sanchez, J.L.Ghadirian, N.Horton, N.C.

(2022) J Virol 96: e0216421-e0216421

  • DOI: https://doi.org/10.1128/jvi.02164-21
  • Primary Citation of Related Structures:  
    7SZX, 7SZY

  • PubMed Abstract: 

    Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the "rolling hairpin" replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication. IMPORTANCE The high-resolution structure of the DNA binding and cleavage domain of the main replicative protein, NS1, from the human-pathogenic virus human parvovirus B19 is presented here. Included also are predictions of how the protein recognizes important sequences in the viral DNA which are required for viral replication. These predictions can be used to further investigate the function of this protein, as well as to predict the effects on viral viability due to mutations in the viral protein and viral DNA sequences. Finally, the high-resolution structure facilitates structure-guided drug design efforts to develop antiviral compounds against this important human pathogen.


  • Organizational Affiliation

    BMCB Graduate Program, University of Arizonagrid.134563.6, Tucson, Arizona, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS1 protein176Human parvovirus B19Mutation(s): 0 
UniProt
Find proteins for A3F778 (Human parvovirus B19)
Explore A3F778 
Go to UniProtKB:  A3F778
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3F778
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.06α = 90
b = 49.1β = 90
c = 74.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-03-30 
  • Deposition Author(s): Horton, N.C.

Funding OrganizationLocationGrant Number
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description