Figure 6.

Model for the secondary structure and domain architecture of the STMV RNA genome derived from SHAPE measurements performed inside intact virions. Thirty representative helices (numbered in brackets) that constitute plausible sites of interaction with capsid protein dimers²¹ are emphasized with colored lines. Three regions with the largest differences relative to the ex virio structure are identified as a, b, and c. The start and stop codons for the capsid protein open reading frame are boxed. Nucleotides are colored by SHAPE reactivity using the scheme shown in Fig. 3. (inset) Schematic map of STMV RNA helices and connectivity superimposed onto icosahedral geometry. Each edge corresponds to an RNA-capsid interaction site.