9YNV | pdb_00009ynv

Histone Acetyl Transferase (HAT) module of ctSAGA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 237.96 kDa 
  • Atom Count: 10,084 
  • Modeled Residue Count: 1,249 
  • Deposited Residue Count: 2,139 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative transcriptional coactivator HFI1 proteinA [auth H]485Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SED0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SED0 
Go to UniProtKB:  G0SED0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SED0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
histone acetyltransferaseB [auth N]405Thermochaetoides thermophilaMutation(s): 0 
EC: 2.3.1.48
UniProt
Find proteins for G0SCB2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SCB2 
Go to UniProtKB:  G0SCB2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SCB2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional adapter 2C [auth M]519Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S7B2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S7B2 
Go to UniProtKB:  G0S7B2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S7B2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinD [auth O]730Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SD59 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SD59 
Go to UniProtKB:  G0SD59
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SD59
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419+SVN
RECONSTRUCTIONPHENIX

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