Human Suv3, a key helicase of Superfamily 2, forms a unique homodimer that partners with the exoribonuclease PNPase to mediate mitochondrial RNA decay and surveillance. Despite its central role in mitochondrial homeostasis, the molecular basis of Suv3’s dimerization and RNA unwinding activity has remained unclear. Here, we present near-atomic resolution cryo-EM structures of Suv3 in four distinct functional states: the apo form, two binary complexes with ADP and single-stranded RNA (ssRNA), and a ternary complex with ssRNA and a non-hydrolyzable ATP analog. These structures reveal that Suv3 adopts an asymmetric dimeric configuration, with the two protomers rotated approximately 110 degrees relative to each other. In the binary complexes, only one protomer binds ADP and ssRNA; in the ternary complex, only one protomer engages both ssRNA and the ATP analog. This asymmetric assembly enables Suv3 to expose a single protomer for interaction with structured RNA, which harbors a long 3′ overhang, thereby facilitating ATP hydrolysis-dependent, processive RNA unwinding. Together, these findings provide critical structural insights into Suv3’s asymmetric dimerization and define the mechanism underlying its role in mitochondrial RNA surveillance and degradation.
Patra et al. (Sun,) studied this question.