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- PDB-9yzy: ctSAGA Focused on HAT Bromodomain region -

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Basic information

Entry
Database: PDB / ID: 9yzy
TitlectSAGA Focused on HAT Bromodomain region
Components
  • Transcriptional adapter 2
  • ctAda3
  • histone acetyltransferase
KeywordsTRANSCRIPTION / ctSAGA complex / Histone Acetyl Transferase (HAT) Module / Tra1 module and Core module
Function / homology
Function and homology information


SAGA-type complex / histone H3 acetyltransferase activity / SAGA complex / histone acetyltransferase complex / histone acetyltransferase / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...SAGA-type complex / histone H3 acetyltransferase activity / SAGA complex / histone acetyltransferase complex / histone acetyltransferase / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Histone acetyltransferase GCN5 / Myb-like domain profile. / SWIRM domain ...Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Histone acetyltransferase GCN5 / Myb-like domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Myb-type HTH DNA-binding domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Myb domain / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / GNAT domain / SANT/Myb domain / Acyl-CoA N-acyltransferase / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional adapter 2 / histone acetyltransferase / Uncharacterized protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsMattoo, R.U.H. / Chen, D.H. / Bushnell, D.A. / Tamir, S. / Kornberg, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049985 United States
CitationJournal: Mol Cell / Year: 2025
Title: Structure of the transcriptional co-activator SAGA complex, including the histone acetyltransferase module.
Authors: Rayees U H Mattoo / Dong-Hua Chen / David A Bushnell / Sagi Tamir / Roger D Kornberg /
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 ...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.
History
DepositionOct 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: histone acetyltransferase
M: Transcriptional adapter 2
O: ctAda3


Theoretical massNumber of molelcules
Total (without water)185,8223
Polymers185,8223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein histone acetyltransferase


Mass: 46983.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SCB2, histone acetyltransferase
#2: Protein Transcriptional adapter 2


Mass: 58866.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S7B2
#3: Protein ctAda3


Mass: 79972.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SD59
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ctSAGA HAT module focused on Bromodomain region / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: HEPES buffer
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 68.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
3SerialEMimage acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 384825 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00267502
ELECTRON MICROSCOPYf_angle_d0.523910137
ELECTRON MICROSCOPYf_chiral_restr0.03951069
ELECTRON MICROSCOPYf_plane_restr0.0051343
ELECTRON MICROSCOPYf_dihedral_angle_d4.15941002

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