6T9I

cryo-EM structure of transcription coactivator SAGA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SPT20A [auth B]604Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P50875 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50875 
Go to UniProtKB:  P50875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50875
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SPT3B [auth C]337Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P06844 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06844 
Go to UniProtKB:  P06844
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06844
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5C [auth D]798Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38129 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38129 
Go to UniProtKB:  P38129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38129
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6D [auth E]516Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53040 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53040 
Go to UniProtKB:  P53040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53040
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9E [auth F]157Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05027 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05027 
Go to UniProtKB:  Q05027
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05027
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10F [auth G]206Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12030 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12030 
Go to UniProtKB:  Q12030
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12030
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional coactivator HFI1/ADA1G [auth H]488Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12060 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12060 
Go to UniProtKB:  Q12060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12060
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12H [auth I]539Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03761 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03761 
Go to UniProtKB:  Q03761
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03761
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional activator SPT7I [auth K]1,332Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35177 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35177 
Go to UniProtKB:  P35177
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35177
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 73J [auth Q]657Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53165 
Go to UniProtKB:  P53165
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53165
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription-associated protein 1K [auth T]3,744Saccharomyces cerevisiae S288CMutation(s): 0 
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
unassigned sequenceL [auth U]155Saccharomyces cerevisiae S288CMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.5
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



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