For a large proportion of the side chains, density was clear and practi-
cally all densities in the core of SAGA and Tra1 could be assigned with
confidence. The single exception to this procedure is the Ada3 domain
at the docking site of the HAT module, where density showed second-
ary structure elements but could not resolve individual side chains.
We cannot therefore exclude errors in amino-acids register for this
domain. Tra1 and the main lobe were separately geometry-optimized
in PHENIX^58 followed by real-space refinement with secondary struc-
ture restraints against the corresponding post-processed maps. This
procedure was repeated after a round of final manual corrections to
the structure in Coot. All display images were generated using UCSF
Chimera^59 and ChimeraX^60.
Reporting summary
Further information on research design is available in the Nature
Research Reporting Summary linked to this paper.
Data availability
The cryo-EM maps have been deposited in the Electron Microscopy
Data Bank (EMDB) under accession codes EMD-10438 (SAGA–TBP),
EMD-10440 (SAGA–TBP, refined for Tra1 lobe), EMD-10441 (SAGA–TBP,
refined for main lobe), EMD-10446 (SAGA–TBP, low-pass-filtered), EMD-
10448 (SAGA–TBP, focused classification on TBP), EMD-10447 (SAGA
without TBP). The model coordinates for SAGA–TBP were deposited
in the Protein Data Bank (PDB) under the accession codes 6TB4 and
6TBM (including Spt8 and DUB).
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Acknowledgements We thank D. Devys and L. Tora for carefully reading the manuscript and
for advice; R. Wagner and B. Séraphin for advice during the initial stages of this project; and R.
Ben-Shem for graphics expertise. We acknowledge support from the Institut National de la
Santé et de la Recherche Médicale (INSERM), the Centre National pour la Recherche
Scientifique (CNRS), the Association pour la Recherche sur le Cancer (ARC), the Ligue contre
le Cancer, ANR-15-CE11-0022-01 and ANR-10-LABX-0030-INRT, a French State fund managed
by the Agence Nationale de la Recherche under the frame program Investissements d’Avenir
ANR-10- IDEX-0002-02. We acknowledge the use of resources of the French Infrastructure for
Integrated Structural Biology FRISBI ANR-10-INBS-05 and of Instruct-ERIC.Author contributions P.S. and A.B.-S. designed the study; A.B.-S. designed the SAGA
purification method and reconstituted the SAGA–TBP complex; A.B.-S. and C.C. defined
conditions for grid preparation and freezing; C.C. and G.P. froze grids; G.P. collected and
analysed cryo-EM data; A.F., G.P. and A.B.-S. interpreted the maps by fitting crystal coordinates
and model building; O.K. purified TBP, TFIIA and SAGA and used them to perform pull-down
and gel-shift assays; P.S. and A.B.-S. supervised the work; G.P. and O.K. prepared figures; and
A.B.-S. and P.S. wrote the manuscript with input from all authors.Competing interests The authors declare no competing interests.Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41586-020-
1944-2.
Correspondence and requests for materials should be addressed to P.S. or A.B.-S.
Peer review information Nature thanks Steve Hahn and the other, anonymous, reviewer(s) for
their contribution to the peer review of this work.
Reprints and permissions information is available at http://www.nature.com/reprints.