4MGU

Crystal structure of Acheta domesticus Densovirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.290 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure and host entry of an invertebrate parvovirus.

Meng, G.Zhang, X.Plevka, P.Yu, Q.Tijssen, P.Rossmann, M.G.

(2013) J Virol 87: 12523-12530

  • DOI: https://doi.org/10.1128/JVI.01822-13
  • Primary Citation of Related Structures:  
    4MGU

  • PubMed Abstract: 

    The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein VP2428Acheta domestica densovirusMutation(s): 0 
UniProt
Find proteins for F2Y986 (Acheta domestica densovirus)
Explore F2Y986 
Go to UniProtKB:  F2Y986
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Y986
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*T)-3')B [auth C]3Acheta domesticus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.290 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 415.469α = 90
b = 415.469β = 90
c = 281.93γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
GLRFphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations