6TBM

Structure of SAGA bound to TBP, including Spt8 and DUB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of SAGA and mechanism of TBP deposition on gene promoters.

Papai, G.Frechard, A.Kolesnikova, O.Crucifix, C.Schultz, P.Ben-Shem, A.

(2020) Nature 577: 711-716

  • DOI: https://doi.org/10.1038/s41586-020-1944-2
  • Primary Citation of Related Structures:  
    6TB4, 6TBM

  • PubMed 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 nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes 1 . 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.


  • Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box Binding Protein (TBP)A [auth M]240Komagataella phaffii GS115Mutation(s): 0 
Gene Names: SPT15
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional coactivator HFI1/ADA1B [auth A]448Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit of SAGA histone acetyltransferase complex698Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0651
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Spt20D [auth F]517Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to actE [auth D]341Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complexF [auth E]1,191Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10G [auth J]217Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit (61/68 kDa) of TFIID and SAGA complexesH [auth K]609Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit (90 kDa) of TFIID and SAGA complexesI [auth G]722Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit (60 kDa) of TFIID and SAGA complexesJ [auth H]485Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiationK [auth I]153Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription-associated protein3,825Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator involved in glucose repression of Gal4p-regulated genesM [auth B]722Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Spt8400Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-BO [auth R]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolaseP [auth Q]502Komagataella phaffii GS115Mutation(s): 0 
EC: 3.4.19.12
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 11Q [auth O]123Komagataella phaffii GS115Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription and mRNA export factor SUS1R [auth P]96Komagataella phaffii GS115Mutation(s): 0 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GLZ
Query on GLZ
O [auth R]L-PEPTIDE LINKINGC2 H5 N OGLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0022-01
French National Research AgencyFranceANR-10-LABX-0030-INRT
French National Research AgencyFranceANR-10-IDEX-0002-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary