Research article
The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases
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* Corresponding author: Bruno Canard Bruno.Canard@afmb.cnrs-mrs.fr
1 Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France
2 Boston Biomedical Research Institute, 64, Grove St, Watertown 02472, MA, USA
BMC Bioinformatics 2005, 6:255 doi:10.1186/1471-2105-6-255
Published: 14 October 2005Additional files
Additional File 1:
Multiple alignment of Flaviviridae RNA polymerase palm subdomains. The conserved motifs are labeled according to the nomenclature described for the RNA polymerase family. Invariant residues are highlighted in red, while conserved residues are boxed yellow highlighted in bold. A consensus sequence with 70% similarity is shown below the alignment. The sequences are sorted by genera.
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Additional File 2:
Ramachandran plot of the GBV-C Model with PROCHECK statistics. A: Ramachandran plot of GBV-C polymerase model. Favoured and allowed regions are
in red and yellow, respectively. All residues are represented by black boxes (■) except
glycine (▲). Red boxes (
) highlight residues in forbidden regions.
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Additional File 4:
Superimposition of the models generated with different programs. A. Models generated using SWISS-MODEL (represented in light blue), and MODELLER: model 1 (represented in light green), model 3 (represented in magenta) or model 2 (represented in yellow) were superimposed. B. 90° rotation view of the same superimposed models. C. Zoom view of the superimposed amino acids of the GTP pocket.
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Additional File 5:
score of the different model generated according to VERIFY3D.
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Additional File 3:
Residues conservation plotted on the structure. Calculated homology based on the superimposition of the structure of HCV polymerase on the GBV-C polymerase model. The figure was done using BOBSCRIPT. The similarity is shown on this structure by a white (low score) to red (identity) colour ramp. The green doted line indicates the position of the disulfide bridge.
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