Structure of the SARS-CoV‑2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

The severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2)
frameshift stimulatory element (FSE) is necessary for programmed −1
ribosomal frameshifting (−1 PRF) and optimized viral efficacy.
The FSE has an abundance of context-dependent alternate conformations,
but two of the structures most crucial to −1 PRF are an attenuator
hairpin and a three-stem H-type pseudoknot structure. A crystal structure
of the pseudoknot alone features three RNA stems in a helically stacked
linear structure, whereas a 6.9 Å cryo-EM structure including
the upstream heptameric slippery site resulted in a bend between two
stems. Our previous research alluded to an extended upstream multibranch
loop that includes both the attenuator hairpin and the slippery site–a
conformation not previously modeled. We aim to provide further context
to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM
approaches, by presenting a 6.1 Å cryo-EM structure featuring
a linear pseudoknot structure and a dynamic upstream multibranch loop.