3N7X

Crystal structure of Penaeus stylirostris densovirus capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structure of Penaeus stylirostris densovirus, a shrimp pathogen.

Kaufmann, B.Bowman, V.D.Li, Y.Szelei, J.Waddell, P.J.Tijssen, P.Rossmann, M.G.

(2010) J Virol 84: 11289-11296

  • DOI: https://doi.org/10.1128/JVI.01240-10
  • Primary Citation of Related Structures:  
    3N7X

  • PubMed Abstract: 

    Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein, the smallest parvoviral capsid protein reported thus far, was determined to 2.5-Å resolution by X-ray crystallography. The structure represents the first near-atomic resolution structure within the genus Brevidensovirus. The capsid protein has a β-barrel "jelly roll" motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the PstDNV coat protein adopts a "domain-swapped" conformation relative to its twofold-related neighbor similar to the insect parvovirus Galleria mellonella densovirus (GmDNV) but in stark contrast to vertebrate parvoviruses. However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein329Decapod penstyldensovirus 1Mutation(s): 0 
Gene Names: capsid protein
UniProt
Find proteins for Q9E2G5 (Penaeus stylirostris penstyldensovirus 1)
Explore Q9E2G5 
Go to UniProtKB:  Q9E2G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9E2G5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.89α = 90
b = 245.471β = 90
c = 268.467γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
envelopephasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-07
    Changes: Other
  • Version 1.3: 2014-07-16
    Changes: Other
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2019-11-27
    Changes: Database references
  • Version 1.6: 2019-12-18
    Changes: Database references
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.1: 2024-04-03
    Changes: Data collection, Refinement description