3N7X

Crystal structure of Penaeus stylirostris densovirus capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1128/JVI.01240-10

  • 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 phospholipa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A
329Penaeus stylirostris penstyldensovirus 1Mutation(s): 0 
Find proteins for Q9E2G5 (Penaeus stylirostris penstyldensovirus 1)
Go to UniProtKB:  Q9E2G5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.278 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 235.890α = 90.00
b = 245.471β = 90.00
c = 268.467γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSrefinement
envelopephasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-07
    Type: Other
  • Version 1.3: 2014-07-16
    Type: Other
  • Version 1.4: 2017-11-08
    Type: Refinement description