9YOL | pdb_00009yol

Tra1 module of ctSAGA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the transcriptional co-activator SAGA complex, including the histone acetyltransferase module.

Mattoo, R.U.H.Chen, D.H.Bushnell, D.A.Tamir, S.Kornberg, R.D.

(2025) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2025.10.025
  • Primary Citation of Related Structures:  
    9YNU, 9YNV, 9YNW, 9YOL, 9YOQ, 9YZY

  • PubMed Abstract: 

    The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, a 1.8 MDa multi-subunit assembly comprising 19 subunits, is required for RNA polymerase II transcription in eukaryotes. The complex consists of four modules: transcription-associated protein 1 (Tra1), core, deubiquitination (DUB), and histone acetyltransferase (HAT). Although the structures of the Tra1, core, and DUB modules have been determined, the overall architecture of the HAT module remained elusive due to its inherent flexibility. To address this, we conducted cryo-electron microscopy (cryo-EM) analyses on SAGA purified from the thermophilic fungus Chaetomium thermophilum, yielding structures of Tra1 and core modules at 2.6 Å and three of the four HAT subunits at 3.7 Å. The structure of the HAT module was informative about the aspects of histone acetylation and the interface of HAT-core modules, contradicting earlier AlphaFold predictions. Our structure-guided genetic and biochemical analyses confirmed the roles of Ada1 and Spt7 in anchoring the HAT module within the SAGA complex.


  • Organizational Affiliation
    • Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: rmattoo@stanford.edu.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SCA7 domain-containing proteinA [auth Q]1,273Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S6A1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S6A1 
Go to UniProtKB:  G0S6A1
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UniProt GroupG0S6A1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spt20-like SEP domain-containing protein1,192Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYM2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0RYM2
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UniProt GroupG0RYM2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chains: C433Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S660 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S660
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transcriptional coactivator HFI1 proteinD [auth H]485Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SED0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SED0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12E [auth I]770Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S2A1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S2A1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Non-specific serine/threonine protein kinaseF [auth A]3,893Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S842 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S842
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UniProt GroupG0S842
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419+SVN
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049985

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release