Journal: Nature / Year: 2020 Title: Structure of SAGA and mechanism of TBP deposition on gene promoters. Authors: Gabor Papai / Alexandre Frechard / Olga Kolesnikova / Corinne Crucifix / Patrick Schultz / Adam Ben-Shem / Abstract: SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to ...SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.
History
Deposition
Oct 31, 2019
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Header (metadata) release
Jan 29, 2020
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Map release
Jan 29, 2020
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
UniProtKB: Spt20-like SEP domain-containing protein
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Macromolecule #5: Subunit of the SAGA and SAGA-like transcriptional regulatory comp...
Macromolecule
Name: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
UniProtKB: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
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Macromolecule #6: Subunit of the SAGA transcriptional regulatory complex, involved ...
Macromolecule
Name: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
UniProtKB: Subunit (60 kDa) of TFIID and SAGA complexes
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Macromolecule #11: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA pol...
Macromolecule
Name: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 52.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 1068534
Startup model
Type of model: EMDB MAP
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354104
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