TFIID

Binding of the general transcription factor TFIID, to the core promoter is the first step in the assembly of the whole transcriptional machinery. Using single particle analysis we obtained a 3-D model of TFIID and TFIID-A-B by negative stain, and located the position of TBP by antibody labeling (Andel et al., Science 1999). We have recently led the implementation of a new statistical method to calculate the 3-D variance and covariance of a cryo-EM reconstruction. This method can identify mobile regions and produce multiple conformationally-distinct models that more accurately mirror the population found in the protein sample. We have first applied this methodology to analysis of the human basal transcription factors TFIID and RNA Pol II. We found that a number of discrete structural elements in TFIID move in a concerted manner via hinges in the structure (Grob et al., Structure 2006). We propose that this type of conformational versatility is likely to be an intrinsic property of large macromolecular complexes and important for their biological function.

TFIID is also far from being biochemically unique. As an example of the importance of compositional variation in TFIID, it is known that proper ovarian development requires the cell type-specific TAF4b subunit. We obtained a 3D reconstruction of a cell type-specific core promoter recognition complex containing TAF4b and TAF4 (4b/4-IID), which is responsible for directing transcriptional synergy between c-Jun and Sp1 at a TAF4b target promoter. Our studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA and putative activator interactions. Importantly, this conformation correlates with differential activator-dependent transcription and promoter recognition by 4b/4-IID.