RPAP3, short for RNA polymerase II-associated protein 3, is a key component of the R2TP co-chaperone complex. The R2TP complex, together with HSP90, is involved in the activation and assembly of multiple macromolecular complexes, such as RNA polymerase II and complexes of the phosphatidylinositol-3-kinase-like family of kinases (PIKKs) like mTORC1 and ATR/ATRIP [1,3,5]. It also seems to be associated with the regulation of miRNA activity and ribosome biogenesis [2,6].

The C-terminal domain of RPAP3, also known as the RUVBL2-binding domain (RBD), is essential for the assembly of R2TP and R2TP-like co-chaperone complexes as it directly interacts with RUVBL2 [1]. In addition, RPAP3 isoform 1, but not isoform 2, interacts with PIH1D1 to form the R2TP complex, and knockdown of RPAP3 isoform 1 down-regulates PIH1D1 protein level [4]. RPAP3 also binds TRBP, and this binding might sequester TRBP to regulate the miRNA pathway [2]. Moreover, the unphosphorylated form of RPAP3 binds ribosomal pre-assembly complexes to modulate ribosome biogenesis, with phosphorylation at specific Ser residues by CK2 affecting this binding [6].

In conclusion, RPAP3 is crucial for the assembly and function of the R2TP co-chaperone complex, playing roles in macromolecular complex assembly, miRNA activity regulation, and ribosome biogenesis. Understanding RPAP3's functions through studies like those on its isoforms, domain interactions, and phosphorylation-related binding can provide insights into these biological processes and potentially related disease mechanisms.