Structural basis for the synergistic assembly of the snRNA export complex

The nuclear cap-binding complex (CBC) and its partner ARS2 play crucial roles in regulating Pol II transcript fate through mutually exclusive interactions with RNA effectors. One such effector, PHAX, mediates the nuclear export of U-rich small nuclear RNAs (snRNAs). Here we present the cryo-EM structure of the snRNA export complex comprising phosphorylated PHAX, CBC, CRM1, Ran-GTP and capped RNA. The central region of PHAX bridges the CBC-bound capped RNA to the CRM1-RanGTP, while also significantly reinforcing cap dinucleotide binding. Additionally, PHAX interacts with a distant region of CRM1 facilitating contacts of an essential phosphorylated region with the prominent basic surface of RanGTP. The importance of these interactions is confirmed by in vitro and in cell mutagenesis experiments. CBC engagement within the snRNA export complex is incompatible with its interactions with other RNA effectors such as ALYREF or NCBP3. Taken together, we demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from the CBC, and commits the complex for export.