SUPPLEMENTARY INFORMATION

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1 Supplementary Table 1. For each experiment the table shows the number of images analyzed, resolution obtained, preparation method used for EM observation, characteristics of the microscope on which the data was collected and the range of defocus values used. Number Experiments of images TFIID-Rap Resolution Holo-TFIID Complex Preparation method Negative stain Microscope, emitter, voltage Philips CM120, LaB6, 120kV Defocus range (um) TFIID-TFIIA- DNA Holo-TFIID Complex TFIID-TFIIA- Rap1-DNA Unstained Cryo-EM FEI Tecnai F20 FEG, 200kV Holo-TFIID Complex I Unstained Cryo-EM FEI Polara, FEG, 300kV Complex II

2 Supplementary Figure 1. a, Field of negatively stained TFIID-Rap1 complexes. Arrows show selected TFIID-complexes. Bar represents 100 nm b, Class average images and corresponding reprojection images of the final 3-D model of the Rap1- TFIID complex. c, Angular distribution of the images used for the final reconstruction. 2

3 Supplementary Figure 2. a, Field of cryo TFIID-TFIIA-DNA complexes observed by cryo EM. Arrows show selected complexes. Bar represents 100 nm. b, Class average images and corresponding reprojection images from the final TFIID-TFIIA-DNA structure. c, Angular distribution of the images used for the final reconstruction. 3

4 Supplementary Figure 3. a. Field of cryo TFIID-TFIIA-Rap1-DNA complexes. Arrows show selected complexes. Bar represents 100 nm. b. Class average images and corresponding reprojection images from the final TFIID-TFIIA-DNA complexes. c. Angular distributions of the images used for the final reconstructions. 4

5 Supplementary Figure 4. Resolution curves for each calculated 3-D model. The criterion used to estimate the resolution corresponds to the intersection point of the half bit curve with the Fourier Shell Correlation (FSC) curve, which was obtained by comparing two distinct reconstructions calculated after splitting the data set in two (Van Heel and Schatz, 2005). The values obtained are reported in Supplementary Table 1. a b c 5

6 a b 6

7 c d Supplementary Figure 5. Density difference maps. The electron density map of each complex was normalized and the corresponding holo-tfiid, which was obtained in the same experimental conditions, was subtracted. For each complex, two different views 7

8 same experimental conditions, was subtracted. For each complex, two different views are shown in the upper and lower row. The first panel of each row represents a 3-D view of the complex, the second panel shows the difference map superimposed to the map of the complex. The positive and negative differences are thresholded at 3σ and represented in red and in meshed blue respectively. The third panel represents the corresponding 3-D view of the holo-tfiid reference model used to calculate the difference. 8

9 Supplementary Figure 6. Assessment of the sorting procedure. a. Fourier-Shell correlation curves before and after sorting of the TFIID-TFIIA-Rap1-DNA dataset. Black line shows the Fourier-shell correlation of the reconstructed structure before sorting. The resolution of Complex I (yellow line) and II (magenta line) are higher, showing that the sorting procedure improved dataset homogeneity. Moreover, the Fourier-Shell correlation between Complex I and II is significantly lower than the value obtained for 9

10 each complex alone indicating that the differences between Complex I and II are significant (Liu et al. 2008). b. Local Multivariate Statistical Analysis (Klaholz et al., 2004) was performed on the non-sorted images to assess whether the key features of complex I (a large B-lobe) and of complex II (a bridge of density between C1 and B- lobes) can be revealed prior to sorting. All images corresponding to a particular TFIID view in which these features are clearly visible were extracted for Complex I (upper left panel) and Complex II (lower left panel). The intensity variations of these images were analysed within a mask (white ellipse) containing the characteristic features (arrows). After partitioning, class average images were obtained representing both holo TFIID (central panels) and the TFIID complexes show the key features (right panels, arrows). This experiment shows that the key features that define Complexes I and II can be revealed prior sorting and thus constitute a prominent variation within the masked area. c. In order to verify that these key features are revealed even if all the images variations are analyzed and not only those occurring within the restricted mask, the same experiment was performed using a large mask encompassing all pixels of the image. The same results were obtained indicating that the key features that define complexes I and II constitute a prominent variation within the whole image. 10

11 Supplementary Figure 7. Immunolocalization of the C-terminus of Taf2. a b c d e a. Specificity of anti-taf2p C-terminal antibody. Purified TFIID (50 and 100 ng amounts; see ref 5) was fractionated by SDS-PAGE, electro-transferred to Immobilon membrane and paired, equivalent strips containing either 50 and 100 ng of TFIID were excised from the membrane. Membranes were blocked and then incubated with a 1/8000 dilution of antigen peptide affinity-purified anti-taf2 IgG derived from the serum of a rabbit (#366) immunized with a carrier-conjugated peptide composing Taf2 amino acids Incubation of the two identical sets of blots was conducted either in the presence of Taf2 C-terminal antigen peptide ( 1342 KVEKQIVKPKVTSKQ 1356 ; C- terminal, blot left), or an unrelated peptide derived from the N-terminus of Taf2 ( 3 SKNATPRAIVSESST 19 ; Unrelated, blot right) present at a calculated 200-fold molar excess (peptide:total IgG) of competitor peptides. Note that both the antigen and 11

12 unrelated peptide had an N-terminal cysteine residue added (not shown). Inclusion of antigen peptide, but not unrelated peptide, effectively blocked antibody binding to Taf2 indicating that the anti-taf2 C-terminal antibody was specific. b. Sensitivity of anti-taf2 C-terminal antibody. TFIID-containing blots generated as described above were incubated with affinity purified anti-taf2 IgG at three dilutions as shown (1:2000; 1:4000; 1:8000). Immunoreactive Taf2 was detected by chemiluminescence; robust signals were detected at all three dilutions indicating high sensitivity. c-e. Immunomapping of C-terminal domain of Taf2 in the TFIID complex. A five-fold molar excess of the antibody was incubated for 20 min on ice with purified TFIID. Images from negative stained immune complexes were collected on a Philips CM120 microscope equipped with a LaB 6 cathode and operating at 120kV. Images were recorded on a CCD camera at a nominal magnification 45,000x. Boxed molecular images were aligned against references projected from a negatively stained TFIID reference structure and clustered into classes corresponding to different views. (c) Class average images in which the TFIID-bound antibody is visible (d) Same views outlined by equidensity contour levels. (e) Corresponding orientation of the 3-D reference model showing that the C-terminus of Taf2 is located in lobe D. The arrows indicate the bound antibody. 12

13 Supplementary Figure 8. Schematic representation of the two DNA fragments used in this study to form the TFIID containing complexes. a, Ad2 MLP promoter fragment; location of five tandem copies of a consensus 17 bp yeast Gal4 binding site, TATA element at -30 relative to the transcription start(initiation) site, TSS shown. Nucleotide sequence numbering relative to the shown TSS. b, Chimeric UAS RAP1 -PGK1 promoter fragment; location of the RPS8A enhancer, containing two tandem Rap1 binding sites, single functional PGK1 TATA box and TSS indicated. Note that the nucleotide coordinates shown are relative to the TSS of this chimeric construct, not those of the natural PGK1 or RPS8A genes. 13

14 Supplementary Figure 9. a. Schematic depiction of the RPS1A promoter fragment used in this supplementary study with indications of the distances between Rap1 binding sites and the TATA like elements (Bendjennat and Weil, 2008). b. Measured loop sizes formed upon incubation of TFIID, TFIIA and Rap1 with the RPS1A promoter fragment. The histogram shows two peaks at 72 and 46 nm, which correlates with the expected sizes of the loops. c. Images showing visible DNA ends (arrows) protruding from the Rap1- TFIID complex after loop formation. 14

15 a b c d Supplementary Figure 10. Image analysis of isolated, negatively stained Rap1 molecules. Purified yeast Rap1 was adsorbed on a carbon coated EM grid and negatively stained according to the sandwich method in which a second 10nm thick carbon film is deposited on top in order to obtain a more homogeneous staining. Images were recorded in low dose conditions using a Philips CM120 electron microscope equipped with a LaB6 cathode and operating at 100 kv. Boxed particles were processed using the IMAGIC software package and the first 3-D model was built using the angular reconstruction method (Van Heel 1987). a. Average views of negatively stained Rap1 molecules. b. Reprojections of the 3-D model of Rap1 15

16 using the angular reconstruction method (Van Heel 1987). a. Average views of negatively stained Rap1 molecules. b. Reprojections of the 3-D model of Rap1 corresponding to the views shown in (a). c. Three-dimensional envelope of the negatively stained Rap1 molecule. The structure of Rap1 shows a 2 lobed horseshoe shape structure. d. The 3-D envelope of Rap1 can be fitted into the additional density found on both sides of lobe B in TFIID-TFIIA-Rap1-DNA Complex II. The size and twolobed organization of Rap1 is similar to the additional density. The bar represents 59 nm in (a) and (b), 6 nm in (c) and 10 nm in (d). 16

17 Supplementary Figure 11. TFIIA point mutations affecting interaction with various activators. The atomic structure of TFIIA (Toa1, dark grey; Toa2, light grey), TBP (ochre), TATA DNA (dark green) and of the Rap1 DNA Binding Domain (dark red) were fitted into the additional density found in the TFIID-TFIIA-Rap1-DNA Complex II. TFIIA mutations that affect activation without interfering with TBP binding are highlighted in its structure (Ozer et al. 1996). Activation was tested with the following activators: Gal4-AH, Gal4-CTF, AP-1, Gal4-VP16 and Zta. The yeast equivalent of TFIIA mutations affecting interaction with all of these activators (Y10A and F71A) are colored red, those influencing only Zta interaction are depicted pink and a mutation that has no effect on Zta binding while abolishing interactions with all other activators are colored green. In yellow a triple mutation toa1-25 is depicted (K255A, R257A and K259A), which is defective for in vitro pol II transcription (Kang et al. 1995). 17

18 Supplementary Figure 12. TFIIA mutants affect DNA loop formation. Three TFIIA mutants were tested for DNA binding efficiency and loop formation within the TFIID- Rap1-TFIIA-DNA complex. The Toa2 mutants Y10A (human equivalent Y6A), F71A (human equivalent F67A) (Ozer et al. 1996) and toa1-25 (Kang et al. 1995) were reported to still bind TBP while being deficient in activated Pol II transcription. DNA 18

19 reported to still bind TBP while being deficient in activated Pol II transcription. DNA binding efficiency and loop formation was measured after platinum shadowing of the nucleoprotein complexes as described in the extended Material and Methods section. All DNA binding experiments were performed on the RPS1A promoter fragment with a TFIID: Rap1: TFIIA: DNA molar ratio of 1:5:5:10 for a. Table showing the proportion of TFIID molecules bound to DNA (DNA binding efficiency) and frequency of DNA loop formation of the TFIID-Rap1-DNA complex in the absence or presence of either wild type or mutant TFIIA. The data shows that the TFIID-Rap1 complex binds less efficiently to DNA in the absence (55%) than in the presence (83%) of wild type TFIIA. The DNA binding efficiency is only slightly restored using the mutant versions of TFIIA (around 65% for all mutants tested). DNA loop formation decreases from 36% to 19% when TFIIA is omitted. TFIIA containing the Toa1-25 and Toa2 F71A variant proteins behave similarly and show intermediate looping frequency, while Y10A is strongly impaired in loop formation. b. Histograms showing the size of the loops formed upon incubation of TFIID, Rap1, DNA without TFIIA (2) and in the presence of the wild type (1) or mutant (3 toa1-25; 4 Toa2-F71A; 5 Toa2-Y10A) TFIIA. All versions of TFIIA shows similar loop size distribution pattern with peaks corresponding to the distances between the Rap1 binding sites and the TA-rich regions on the RPS1A promoter (see Supplementary Figure 9), whereas these peaks disappear in the absence of TFIIA. 19

20 Supplementary references Bendjennat M, Weil P.A. (2008) The transcriptional repressor activator protein Rap1p is a direct regulator of TATA-binding protein. J Biol Chem. 283, Kang JJ, Auble DT, Ranish JA, Hahn S. (1995) Analysis of the yeast transcription factor TFIIA: distinct functional regions and a polymerase II-specific role in basal and activated transcription. Mol Cell Biol. 15: Klaholz BP, Myasnikov AG, Van Heel M. (2004) Visualization of release factor 3 on the ribosome during termination of protein synthesis. Nature 427, Liu WL, Coleman RA, Grob P, King DS, Florens L, Washburn MP, Geles KG, Yang JL, Ramey V, Nogales E, Tjian R. Structural changes in TAF4b-TFIID correlate with promoter selectivity. Mol. Cell 29, Ozer J, Bolden AH, Lieberman PM. (1996) Transcription factor IIA mutations show activator-specific defects and reveal a IIA function distinct from stimulation of TBP-DNA binding. J Biol Chem. 271, Van Heel M. (1987) Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21, Van Heel M, Schatz M. (2005) Fourier shell correlation threshold criteria. J Struct Biol. 151,