Primary Citation PubMed: 11884572
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The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases.
(2005) BMC Bioinformatics 6
PubMed: 16225688 | PubMedCentral: PMC1283970 | DOI: 10.1186/1471-2105-6-255
The three dimensional model of the GBV-C RdRp was constructed using the crystal structure coordinates of the HCV polymerase [ 8 , 7 ] (PDB code: 1GX5, 1QUV).
For this study we have used different structures of HCV (PDB code: [1GX5, 1GX6]), and BVDV (PDB code: [1S48, 1S49]).
Publication Year: 2005
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation.
(2009) Nucleic Acids Res 37
PubMed: 19468045 | PubMedCentral: PMC2703942 | DOI: 10.1093/nar/gkp351
Output of search of chameleon sequences with the highest non-native P(helix) and non-native P(β) values Sequence Secondary structure PDB Chain SCOP CSSP (for native structure) Non-native P(hel... x) Non-native P(β) Relative P(helix) Relative P(β) LRRARAA CCCCCCC 1cer O d.81.1.1 0.18 0.69 0.13 3.93 0.73 KQMLAKA CCCCCCC 1goj A c.37.1.9 0.13 0.68 0.18 5.10 1.33 QEQLEKA CCCCCCC 1gx5 A e.8.1.4 0.17 0.68 0.13 3.89 0.77 AKEAAQK CCCCCCC 1g9l A a.144.1.1 0.2 0.68 0.1 3.50 0.53 ARAQARQ CCCEEEE 1omh A d.89.1.5 0.14 0.68 – 4.77 – AVIVVFD CCCCCCC 1bgx T c.120.1.2 0.15 0.22 0.58 1.45 3.80 VTVTVFD CCCCCCC 1eu1 A b.52.2.2 0.3 0.12 0.57 0.41 1.88 VFEVNIR HHHHHHH 1nxc A a.102.2.1 0.23 – 0.57 – 2.52 VYWFTVE HHHCCCC 1toh – d.178.1.1 0.22 – 0.57 – 2.54 VYVVFSV CCCCCCC 1vho A c.56.5.4 0.16 0.23 0.57 1.45 3.52 By searching the fragment DB, one can quantitatively analyze non-native secondary structure propensities in comparison with native secondary structure patterns.
Publication Year: 2009
De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5.
(2011) PLoS One 6
PubMed: 21490973 | PubMedCentral: PMC3072391 | DOI: 10.1371/journal.pone.0018515
A number of crystal structures of the HCV polymerase (i.e. 1GX5, 1NHU, 1NHV, 1OS5, 1YVZ, 2BRL, 2D3U, 2D3Z, 2D41, 2DXS, 2GIR, 2HAI, 2HWH, 2HWI, 2I1R, 2JC0, 2O5D, 2WCX, 2WHO, 3CJ0, 3CJ2, 3CJ3, 3CJ4, 3CJ... , 3FRZ and 3HVO), show that the αT helix is close to a site of interaction for non-nucleoside inhibitors.
Publication Year: 2011
PubMed ID is not available.
Published in 2015
A model of the initiation complex is shown in Fig 2B ; in this model a 4-mer ssRNA substrate, taken from the complex structure of the related ɸ6-RdRp (PDB 1HI0) [ 48 ], and rNTP modeled at the... priming site (P-site) and catalytic site (C-site) based on the HCV RdRp complex structure (PDB 1GX5) [ 40 ] can be accommodated in the WNV NS5 RdRp active site with minimal steric clashes with the protein atoms.
Publication Year: 2015
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