6T9J

SAGA Tra1 module


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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 the transcription coactivator SAGA.

Wang, H.Dienemann, C.Stutzer, A.Urlaub, H.Cheung, A.C.M.Cramer, P.

(2020) Nature 577: 717-720

  • DOI: https://doi.org/10.1038/s41586-020-1933-5
  • Primary Citation of Related Structures:  
    6T9I, 6T9J, 6T9K, 6T9L

  • PubMed Abstract: 

    Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) 1,2 and transcription factor IID (TFIID) 2-4 . SAGA is required for all regulated transcription 5 and is conserved among eukaryotes 6 . SAGA contains four modules 7-9 : the activator-binding Tra1 module, the core module, the histone acetyltransferase (HAT) module and the histone deubiquitination (DUB) module. Previous studies provided partial structures 10-14 , but the structure of the central core module is unknown. Here we present the cryo-electron microscopy structure of SAGA from the yeast Saccharomyces cerevisiae and resolve the core module at 3.3 Å resolution. The core module consists of subunits Taf5, Sgf73 and Spt20, and a histone octamer-like fold. The octamer-like fold comprises the heterodimers Taf6-Taf9, Taf10-Spt7 and Taf12-Ada1, and two histone-fold domains in Spt3. Spt3 and the adjacent subunit Spt8 interact with the TATA box-binding protein (TBP) 2,7,15-17 . The octamer-like fold and its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt distinct conformations. Taf12 and Spt20 form flexible connections to the Tra1 module, whereas Sgf73 tethers the DUB module. Binding of a nucleosome to SAGA displaces the HAT and DUB modules from the core-module surface, allowing the DUB module to bind one face of an ubiquitinated nucleosome.


  • Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SPT20A [auth B]604Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT20ADA5YOL148C
UniProt
Find proteins for P50875 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50875 
Go to UniProtKB:  P50875
Entity Groups  
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UniProt GroupP50875
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12B [auth I]539Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAF12TAF61TAF68YDR145WYD8358.02
UniProt
Find proteins for Q03761 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03761 
Go to UniProtKB:  Q03761
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UniProt GroupQ03761
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription-associated protein 1C [auth T]3,744Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRA1YHR099W
UniProt
Find proteins for P38811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38811 
Go to UniProtKB:  P38811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38811
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.5
MODEL REFINEMENTPHENIX1.16

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860, SPP1935, EXC 2067/1-390729940
European Research CouncilGermany693023

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: 2024-05-22
    Changes: Data collection, Database references