Molecular structure of promoter-bound yeast TFIID

Abstract

Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.

Fig. 1

Purification and interaction map of yeast TFIID. a Colloidal coomassie blue stained SDS-PAGE analysis of TFIID complex purified from the SBP-tagged Taf2 strain. b Schematic representation of the TFIID subunits showing the conserved structural domains (colored boxes) and the yeast specific domains (red bars). TBP-BD: TBP binding domain (TAND), Taf7 ID: Taf7 interacting domain, APD: aminopeptidase, HFD: Histone fold domain, INS: Insertion, CCTD: conserved C-terminal domain, NTD: N-terminal domain, WD40: structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide, HEAT: structural motif composed of two alpha helices linked by a short loop, P-rich: proline rich domain, TAF1-BD: Taf1 binding domain, 2ID: Taf2 interacting domain, CR conserved HFD flanking region, YEATS: Yaf9, ENL, AF9, Taf14, Sas5 domain. c Subunit-subunit cross-linking map. Line transparency corresponds to the number of cross-links identified between the two subunits

Fig. 2

Structural organization of yeast TFIID a Cryo-EM model of the yeast Komagataella phaffii TFIID at a resolution of 12.1 Å. b Cryo-EM model of the TFIID-TFIIA-pGAP complex

Fig. 3

Subunit arrangement within the Taf2 lobe a Atomic model docking of the amino-peptidase-like domains of Taf2 (from D1 to D4), the predicted Taf8 helices, and the Taf14 YEATS domain within the Taf2 lobe reconstructed at 4.5 Å resolution. b Linker between the Taf2 lobe and the Twin lobe consisting of two Taf6 HEAT repeats

Fig. 4

Subunit arrangement of the Twin lobe a Atomic model docking of the Taf5 WD40 repeat, Taf5 NTD, Taf6-9, Taf11-13 and Taf4-12 HF domain heterodimers within the Twin lobe. b Central role of the Taf5-WD40 repeat in organizing the HF domain heterodimers. c Structural homology between the Taf6-9-4-12-11-13 HF domain hexamer (ribbons) and the archaeal histone hexamer (tubes). d Linker between the Twin lobe and the Taf1 lobe consisting of two Taf5 NTDs

Fig. 5

Predicted organization of the Taf1 lobe and DNA interactions a Organization of the Taf1 lobe as derived from Volta Phase Plate images of frozen hydrated TFIID-TFIIA-pGAP complexes. The position of the second Taf5-6-9-4-12 module could be determined (green domain). The putative Taf1 flexible domain (grey) is facing the Taf2-bound DNA. b TFIID-DNA interactions within the Taf2 lobe. c TFIID-DNA interactions within the Twin lobe. d Proposed arrangement of the fitted atomic models and subunits in yeast TFIID