2E0Z

Crystal structure of virus-like particle from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus Provides Insight into the Evolution of Viruses

Akita, F.Chong, K.T.Tanaka, H.Yamashita, E.Miyazaki, N.Nakaishi, Y.Suzuki, M.Namba, K.Ono, Y.Tsukihara, T.Nakagawa, A.

(2007) J.Mol.Biol. 368: 1469-1483

  • DOI: 10.1016/j.jmb.2007.02.075

  • PubMed Abstract: 
  • Pyrococcus furiosus is a hyperthermophilic archaeal microorganism found near deep-sea thermal vents and its optimal growth temperature of 100 degrees C. Recently, a 38.8-kDa protein from P. furiosus DSM 3638 was isolated and characterized. Electron m ...

    Pyrococcus furiosus is a hyperthermophilic archaeal microorganism found near deep-sea thermal vents and its optimal growth temperature of 100 degrees C. Recently, a 38.8-kDa protein from P. furiosus DSM 3638 was isolated and characterized. Electron microscopy revealed that this protein aggregated as spheres of approximately 30 nm in diameter, which we designated P. furiosus virus-like particles (PfVs). X-ray crystallographic analysis at 3.6-A resolution revealed that each PfV consisted of 180 copies of the 38.8-kDa protein and retained T=3 icosahedral symmetry, as is often the case in spherical viruses. The total molecular mass of each particle was approximately 7 MDa. An examination of capsid structures suggested strong evolutionary links among PfV, tailed double-stranded DNA bacteriophages, and herpes viruses. The similar three-dimensional structures of the various coat proteins indicate that these viral capsids might have originated and evolved from a common ancestor. The structure of PfV provides a previously undescribed example of viral relationships across the three domains of life (Eukarya, Bacteria, and Archaea).


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Virus-like particle
A, B, C
345Pyrococcus furiosusMutation(s): 0 
Gene Names: PfV
Find proteins for Q401P1 (Pyrococcus furiosus)
Go to UniProtKB:  Q401P1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 631.500α = 90.00
b = 631.500β = 90.00
c = 351.300γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
HKL-2000data collection
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-11-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance