Structural analysis of the yeast exosome Rrp6p–Rrp47p complex by small-angle X-ray scattering

•We show that S. cerevisiae Rrp6p and Rrp47p stabilise each other in vitro.•We determine molecular envelopes of the Rrp6p–Rrp47p complex by SAXS.•Rrp47p binds at the top of the Rrp6p exonuclease domain.•Rrp47p modulates the activity of Rrp6p on a variety of RNA substrates.•Rrp47p does not affect RNA affinity by Rrp6p. The RNase D-type 3′–5′ exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.