9YNU | pdb_00009ynu

Tra1 and core modules including core tip of ctSAGA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 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 85: 4333-4346.e4

  • 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))
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UniProt GroupG0S6A1
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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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UniProt GroupG0RYM2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein433Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S660 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5767Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SH10 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SH10
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6480Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S770 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transcription initiation factor277Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10204Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYR4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transcriptional coactivator HFI1 protein485Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SED0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12770Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S2A1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA complex subunit Spt7J [auth K]1,224Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0016160
UniProt
Find proteins for G0S267 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Non-specific serine/threonine protein kinaseK [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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UniProt GroupG0S842
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419+SVN
RECONSTRUCTIONRELION

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
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references