Figure 4.

(A) The methyl group resonance intensities of Rrp42 resonances in the RNA free exosome divided by the corresponding resonance intensity in the presence of RNA. High bars indicate significant line broadening upon RNA binding, notably observed for residues Ile 71, Ile 85 and Val 137 of Rrp42. The line broadening is shown for three different temperatures, 50, 30 and 20°C. Note that a large number of resonances are not affected by the interaction with RNA (below the dashed bar). (B) Methyl TROSY NMR spectrum of the isoleucine region of the exosome that contains NMR active groups in Rrp41 and Rrp42. NMR spectra in the absence (black) and presence (red) of RNA are shown and a number of assignments are indicated. Regions that are highlighted with a dashed box correspond to resonances in Rrp41 that experience large CSPs upon interaction with the RNA substrate. Spectra were recorded at 323 K. (C) Structure of the Sulfolobus solfataricus exosome (PDB: 2C38) (27) superimposed onto the RNA substrate (in red) visible in the structure of the Pyrococcus abyssi exosome (35) (PDB: 2PO1). Assigned residues that show CSPs in the presence of RNA are indicated in blue. Only a single RNA is present per hexameric exosome complex, as the narrow entrance pore does not allow for the recruitment of multiple substrates simultaneously.