FIGURE 6.

The native secondary structure and tertiary structure of the core encapsidation signaling RNA of the Molney murine leukemia virus. (A) The native secondary structure. (B) The native tertiary structure taken from the first NMR model in the PDB databank (PDB 1S9S; http://www.wwpdb.org/). (C) The tertiary structure predicted by pk3D. The helices are numbered from 1 to 6, in the direction from the 5′ end to the 3′ end, and are colored in the order of red, green, blue, yellow, magenta, and cyan, respectively. The orange spheres in B show the positions of the phosphorus atoms in the first nucleotide G1 for all of the first 20 models given by the NMR experiments. The diverse positions demonstrate the experimentally observed large flexibility of the first helix. The gray segment in the upper-right region in B connecting the fourth and fifth helices shows the conformation of the bulge loop G62-A65 determined by the experiments.