3P0S

Crystal structure of Bombyx mori densovirus 1 capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of Bombyx mori densovirus 1, a silkworm pathogen.

Kaufmann, B.El-Far, M.Plevka, P.Bowman, V.D.Li, Y.Tijssen, P.Rossmann, M.G.

(2011) J Virol 85: 4691-4697

  • DOI: https://doi.org/10.1128/JVI.02688-10
  • Primary Citation of Related Structures:  
    3P0S

  • PubMed Abstract: 

    Bombyx mori densovirus 1 (BmDNV-1), a major pathogen of silkworms, causes significant losses to the silk industry. The structure of the recombinant BmDNV-1 virus-like particle has been determined at 3.1-Å resolution using X-ray crystallography. It is the first near-atomic-resolution structure of a virus-like particle within the genus Iteravirus. The particles consist of 60 copies of the 55-kDa VP3 coat protein. The capsid protein has a β-barrel "jelly roll" fold similar to that found in many diverse icosahedral viruses, including archaeal, bacterial, plant, and animal viruses, as well as other parvoviruses. Most of the surface loops have little structural resemblance to other known parvovirus capsid proteins. In contrast to vertebrate parvoviruses, the N-terminal β-strand of BmDNV-1 VP3 is positioned relative to the neighboring 2-fold related subunit in a "domain-swapped" conformation, similar to findings for other invertebrate parvoviruses, suggesting domain swapping is an evolutionarily conserved structural feature of the Densovirinae.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP494Bombyx mori densovirus 1Mutation(s): 0 
UniProt
Find proteins for Q8V0M6 (Bombyx mori densovirus 1)
Explore Q8V0M6 
Go to UniProtKB:  Q8V0M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8V0M6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 245.4α = 59.98
b = 245.6β = 67.93
c = 245.7γ = 72.27
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
CNSphasing
AVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description