RPB3 has been proposed to be analogous to the a-subunit of the E. coli polymerase. Similarities include molecular size (SDS PAGE: a-40kDa, RPB3-45kDa) certain conserved amino acid sequences, stoichiometry, and role in assembly (Young 1991). Researchers propose the function of RPB3 may be to "nucleate assembly of the enzyme" as mutation of the gene leads to accumulation of certain subunit complexes (Young 1991).
It is important to note that Young and colleagues identified 10 of the 12 subunits of yeast RNA polymerase II by epitope tagging RPB3. They introduced the modified gene into cells lacking RPB3 and used antibodies to precipitate the enzyme (Weaver 1999). The previously radiolabled proteins were separated on SDS PAGE and identified by autoradiography. As this reaction was only a single-step purfication, only 10 subunits were identified (Weaver 1999).