6T9L

SAGA DUB module bound to a ubiqitinated nucleosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 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 ...

    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. pcramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
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Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591
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Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
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Histone H2B 1.1122Xenopus laevisMutation(s): 0 
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UniProt GroupP02281
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Entity ID: 5
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Histone H2B125Xenopus laevisMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBP8, YMR223W, YM9959.05
EC: 3.4.19.12
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Entity ID: 9
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Transcription and mRNA export factor SUS196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUS1, YBR111W-A
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Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
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SAGA-associated factor 1199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF11, YPL047W
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Entity ID: 11
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SAGA-associated factor 73657Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF73, YGL066W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-C76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
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PHAROS:  P0CG48
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Widom601 DNA (145-MER)145synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Widom601 DNA (145-MER)145synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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