Figure 6.

Three-dimensional modeling of inter-molecular ATP synthase complex and RV 3′UTR interaction. A, estimated binding strength between UGUGACC sequences and selected viral or host proteins using HDOCK algorithm. Low RMSD score favors strong binding between the ligand (RNA) and target protein. Cul3 stands for cullin-3, a host E3 ligase protein that does not interact with RNA molecules. B, top view of PyMOL modeling of RV 3′UTR sequences sticking into the head domain of ATP synthase complex (trimeric ATP5A1-ATP5B subunits). C, close-up details of B revealing the nucleotides and possible interacting amino acids.