6TB4

Structure of SAGA bound to TBP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    Université de Strasbourg, Illkirch, France. adam@igbmc.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box Binding Protein (TBP)A [auth M]243Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0183
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional coactivator HFI1/ADA1B [auth A]448Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_FragB_0044
UniProt
Find proteins for C4QZA3 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SAGA-associated factor 73 (Sgf73)C698Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0651
UniProt
Find proteins for C4QZ39 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Spt20D [auth F]517Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0620
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to actE [auth D]341Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0051
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complexF [auth E]1191Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0713
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10G [auth J]217Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0182
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit (61/68 kDa) of TFIID and SAGA complexesH [auth K]609Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0588
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit (90 kDa) of TFIID and SAGA complexesI [auth G]722Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0453
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit (60 kDa) of TFIID and SAGA complexesJ [auth H]485Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-1_0095
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiationK [auth I]153Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0142
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Find proteins for C4QZS5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription-associated proteinL3825Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0571
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Find proteins for C4QYV4 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional adapter 3 (Ada3)M [auth B]76Komagataella phaffii GS115Mutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Source and taxonomy