Experimental Data Snapshot

  • Resolution: 3.60 Å
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 

Starting Model: experimental
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The structure of an insect parvovirus (Galleria mellonella densovirus) at 3.7 A resolution.

Simpson, A.A.Chipman, P.R.Baker, T.S.Tijssen, P.Rossmann, M.G.

(1998) Structure 6: 1355-1367

  • DOI: https://doi.org/10.1016/s0969-2126(98)00136-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Parvoviruses infect vertebrates, insects and crustaceans. Many arthropod parvoviruses (densoviruses) are highly pathogenic and kill approximately 90% of the host larvae within days, making them potentially effective as selective pesticides. Improved understanding of densoviral structure and function is therefore desirable. There are four different initiation sites for translation of the densovirus capsid protein mRNA, giving rise to the viral proteins VP1 to VP4. Sixty copies of the common, C-terminal domain make up the ordered part of the icosahedral capsid. The Galleria mellonella densovirus (GMDNV) capsid protein consists of a core beta-barrel motif, similar to that found in many other viral capsid proteins. The structure most closely resembles that of the vertebrate parvoviruses, but it has diverged beyond recognition in many of the long loop regions that constitute the surface features and intersubunit contacts. The N termini of twofold-related subunits have swapped their positions relative to those of the vertebrate parvoviruses. Unlike in the vertebrate parvoviruses, in GmDNV there is no continuous electron density in the channels running along the fivefold axes of the virus. Electron density corresponding to some of the single-stranded DNA genome is visible in the crystal structure, but it is not as well defined as in the vertebrate parvoviruses. The sequence of the glycine-rich motif, which occupies each of the channels along the fivefold axes in vertebrate viruses, is conserved between mammalian and insect parvoviruses. This motif may serve to externalize the N-terminal region of the single VP1 subunit per particle. The domain swapping of the N termini between insect and vertebrate parvoviruses may have the effect of increasing capsid stability in GmDNV.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN437Galleria mellonella densovirusMutation(s): 0 
Find proteins for Q90125 (Galleria mellonella densovirus)
Explore Q90125 
Go to UniProtKB:  Q90125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90125
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 Å
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.44α = 90
b = 264.44β = 90
c = 683.45γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-04-03
    Changes: Data collection, Refinement description