2J6C

crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Afv3-109, a Highly Conserved Protein from Crenarchaeal Viruses.

Keller, J.Leulliot, N.Cambillau, C.Campanacci, V.Porciero, S.Prangishvili, D.Forterre, P.Cortez, D.Quevillon-Cheruel, S.Van Tilbeurgh, H.

(2007) Virol J. 4: 12

  • DOI: 10.1186/1743-422X-4-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent dat ...

    The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 A resolution. The structure of AFV3-109 is a five stranded beta-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.


    Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS-UMR 8619, Université Paris 11, IFR115, Bâtiment 430, 91405 Orsay, France. Jenny.Keller@u-psud.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AFV3-109
A
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.770α = 90.00
b = 83.528β = 90.00
c = 33.989γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance