712 | Nature | Vol 577 | 30 January 2020
Article
which was absent in a separate map of SAGA lacking TBP (Extended Data
Fig. 3a–d). Local classification revealed sufficient secondary struc-
tural features to guide the precise positioning of cTBP. Site-specific
cross-linking and documented mutations resolved any ambiguity in
orientation arising from the pseudosymmetric fold of cTBP^21 ,^22. A disc-
shaped density neighbouring TBP was assigned to the WD40 protein
Spt8, which was shown to interact with TBP^23 (Extended Data Fig. 3e,
f ). At the opposite pole of the main lobe, the DUB crystal structure fits
into and occupies a large but not well-resolved density that is nearly
completely detached from and independent of SAGA. The DUB mod-
ule is connected to the main lobe by a narrow, elongated density that
contacts the surface of SAGA proximal to the Spt20 SEP domain and the
LisH domain of Taf5 (Fig. 1a, b, Extended Data Fig. 1). The HAT enzymatic
module adopts multiple conformations and orientations. Accordingly,
the bulk of this module is visible only as an elongated featureless density
at the tip of our map. Nevertheless, we could identify its docking site
on SAGA, where two helical domains—attributable to Ada3—lie at the
surface of the Taf6 HEAT-repeats domain.Taf5 orchestrates the main lobe
The main lobe is dominated by the seven-blade WD40 propeller of Taf5
(Fig. 1c). This domain occupies a central position, serving as a structural
hub that connects all major SAGA functions. The flat top face of the
propeller disc clamps together the Taf5 N-terminal domain (NTD) and
the Taf6 HEAT repeats that bind the HAT module. The opposite bottom
face of WD40 holds the histone-fold machinery that ultimately binds
TBP and connects to the DUB module and Tra1.
The positions of the Taf5 NTD and Taf6 HEAT repeats are markedly
different in SAGA compared with TFIID^19 , as these domains assume dif-
ferent roles in establishing connections to the enzymatic DUB (the LisH
extension of Taf5 NTD) and HAT (Taf6) modules (Fig. 1c, Extended Data
Fig. 4). Compared with TFIID, the Taf5 NTD in SAGA makes a rotation
of almost 180 degrees around the WD40 domain, and the Taf6 HEAT
repeats, which are remote in TFIID, are relocated to the vicinity of the
top face of WD40 in SAGA. Notably, unlike SAGA, TFIID harbours two
copies of Taf5 and Taf6 that are held together by homodimerization of
Taf5 NTDs and Taf6 HEAT repeats. As a result of all these variations and
additional interactions with SAGA-specific subunits, the Taf5 WD40
environment is very different in SAGA compared with TFIID.
The ability of Taf6 HEAT repeats to occupy three different positions in
SAGA and TFIID relative to the histone fold is afforded by a 136-residue
linker between these two domains. The Taf6 linker partially encircles
the Taf5 WD40 domain (Fig. 1c), and its position is stabilized by several
interactions along its trajectory. Most notably, the Taf6 linker residues
T135–L141 add a β-strand to the last blade of the WD40 propeller, form-
ing an inter-protein β-sheet.
WD40 domains are recognized as potential hubs that mediate pro-
tein–protein interactions. The Taf5 WD40 in SAGA is a noteworthy
demonstration of this capacity, as it associates with at least 11 different
protein domains (Fig. 1c, d). Taf5 is thus a centrally located master hub
that orchestrates the architecture of the entire main lobe.A deformed histone-fold octamer
An octamer consisting of four histone-fold pairs arranged in a disc-
shaped spiral, similar to the nucleosomal histone octamer, has been
proposed to reside in TFIID and SAGA^24 ,^25. Our structure presents an
atomic model of the full histone-fold octamer that resides at the core of
SAGA and, most probably with minor variations, in the TBP-binding lobe
of TFIID (Fig. 2a). It reveals a disparity between histone-fold interactions
in SAGA compared with the nucleosome, particularly regarding the
incorporation into SAGA of the TBP-binding subunit Spt3, a homologue
of the TFIID Taf11–Taf13 histone-fold pair^24 (Supplementary Video 2).
In the nucleosome, the interaction between neighbouring histone
pairs is mediated by a tightly packed four-helix bundle composed of
helices α2 and α3 of one histone from each pair^26. The SAGA histone-
fold pairs are organized along the spiral in the following order: Taf6–
Taf9, Taf12–Ada1, Spt7–Taf10 and Spt3, which contains two histone
folds, one at each of its ends: nSpt3-HF and cSpt3-HF. Whereas all other
histone-fold pairs are oriented as in the nucleosome, the Spt3 pair is
tilted by 20 degrees compared with its analogous nucleosome H2A–
H2B histone pair (Fig. 2b). This tilt prevents participation of the Taf10
α3-helix in the interaction, shears the four-helix bundle and therefore
nearly completely frees Spt3 from its association with the histone-fold
octamer. The remaining contact is facilitated by a slight tilt in Taf10 and
maintained by only very few bonds between Spt3 and Taf10 residues
(Fig. 2c). To secure incorporation of Spt3 into SAGA, the C-terminal tail
of Spt3 inserts into the centre of the spiral disc (a void volume in the
nucleosome), makes a near complete circle and forms single bonds
with each of the other histone folds in SAGA (Fig. 2d).Ada1Spt2 0Sgf73Taf12Taf6DUBDUBHATTaf5TBPSpt3Ada3Taf10
Spt7 Spt8Tra1a b90°Taf9Tra1Main90°TBPTaf5 WD 40Taf6 HEAT
Taf5 NTDc HATDUBTaf6 linkerTaf5
LisH
Histone fold octamerTaf6 HEAT Taf6 linkerTaf5 NTD
Ada1Spt7
Taf10Taf9Spt2 0
Taf5 NTDTaf6
HEATAda1Spt7Spt2 0Taf6 linkerdTaf6 HF180°Fig. 1 | Structure of the yeast SAGA–TBP complex. a, Front (top) and side
(bottom) views of a composite cryo-EM reconstruction of the yeast SAGA–TBP
complex. Maps from focused refinements of Tra1 (tan), DUB (light pink), Spt8
(white), the main lobe and TBP (blue-green) were combined. HAT density
(light green) is taken from the low-pass-filtered map of the full complex.
b, Corresponding views of the atomic model of the SAGA–TBP complex
focusing on the main lobe. c, The Taf5 WD40 domain structurally orchestrates
the main lobe. Orientation as in a (top). d, Intricate network of protein contacts
with the Taf5 WD40 domain (white).