Skip to main content
. Author manuscript; available in PMC: 2011 Jun 22.
Published in final edited form as: Biochemistry. 2010 Jun 22;49(24):4931–4933. doi: 10.1021/bi100142y

Figure 3.

Figure 3

RNA structure prediction for the pseudoknot domain of the HCV IRES. (A) Secondary structure (10). (B) Predicted structure of the uncomplexed pseudoknot domain. Spheres indicate phosphate positions; nucleotides are colored as shown in panel A. (C) HCV-PK model placed into the electron density of the IRES-ribosome complex (12b). (D) Superposition of hydroxyl radical protection data (11) on the HCV-PK RNA model. Spheres correspond to protected sugar pseudo-atoms; red and yellow indicate strong and moderate protection, respectively.