Extended Data Fig. 3: Fitting of TBP and Spt8 into the cryo-EM map.

a, Pairwise alignment of TBP from P. pastoris and S. cerevisiae. Eight residues (out of 180) differ between the two organisms within the conserved C-terminal part of TBP (marked by a dotted line). These residues are mapped on the structure of cTBP (PDB: 1YTF). None of these residues occur in regions that contact SAGA (highlighted in red). b, Pairwise alignment of TFIIA subunits, Toa1 and Toa2, from P. pastoris and S. cerevisiae. The evolutionary conserved and structured domains of TFIIA (marked by dotted lines) show 60% identity and 80% similarity between the two organisms. It is worth noting that TBP and TFIIA have both been shown to be highly similar even across large evolutionary distances. For example, TBP, as well as Toa2, from yeast and human are functionally interchangeable in Pol II transcription^61,62,63 and yeast TFIIA complements a mammalian in vitro transcription system depleted of TFIIA⁴³. Hence, TBP and TFIIA from S. cerevisiae, which are easier to overproduce in E. coli, are valid substitutes in our experimental system for their homologues from the closely related budding yeast P. pastoris. c, Cryo-EM reconstructions determined in the presence (green) and in the absence (pink) of TBP. The enlarged panel shows the superimposition of both maps and highlights the additional density corresponding to TBP. d, Fitting of the cTBP crystal structure into the additional density observed in the SAGA–TBP complex. The α-loop denotes an α-helix from the linker connecting the two histone folds in Spt3. e, f, Fitting of the WD40 repeat of subunit Spt8 into the cryo-EM map of the SAGA–TBP complex next to TBP.