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- PDB-9yoq: Core module of ctSAGA -

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Basic information

Entry
Database: PDB / ID: 9yoq
TitleCore module of ctSAGA
Components
  • (Putative transcriptional ...) x 2
  • (Transcription initiation factor TFIID subunit ...) x 4
  • Non-specific serine/threonine protein kinase
  • Putative transcription initiation factor
  • SCA7 domain-containing protein
  • Spt20-like SEP domain-containing protein
  • Uncharacterized protein
KeywordsTRANSCRIPTION / ctSAGA complex / Histone Acetyl Transferase (HAT) Module / Tra1 module and Core module
Function / homology
Function and homology information


RITS complex assembly / regulatory ncRNA-mediated heterochromatin formation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / NuA4 histone acetyltransferase complex / RNA polymerase II preinitiation complex assembly / translation initiation factor activity / TBP-class protein binding ...RITS complex assembly / regulatory ncRNA-mediated heterochromatin formation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / NuA4 histone acetyltransferase complex / RNA polymerase II preinitiation complex assembly / translation initiation factor activity / TBP-class protein binding / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / chromatin organization / transcription by RNA polymerase II / transcription coactivator activity / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SAGA-associated factor 73 / LisH / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SAGA-associated factor 73 / LisH / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Spt20-like SEP domain-containing protein / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 12 domain-containing protein / Uncharacterized protein / SCA7 domain-containing protein / TBP-associated factor 6 / Non-specific serine/threonine protein kinase / Putative transcriptional coactivator HFI1 protein / Transcription initiation factor TFIID subunit-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 13, 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
A: Non-specific serine/threonine protein kinase
B: Spt20-like SEP domain-containing protein
C: Uncharacterized protein
D: Transcription initiation factor TFIID subunit 5
E: Transcription initiation factor TFIID subunit 6
G: Transcription initiation factor TFIID subunit 10
H: Putative transcriptional coactivator HFI1 protein
I: Transcription initiation factor TFIID subunit 12
K: Putative transcriptional activator protein
Q: SCA7 domain-containing protein
F: Putative transcription initiation factor


Theoretical massNumber of molelcules
Total (without water)1,230,76611
Polymers1,230,76611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules ABCQF

#1: Protein Non-specific serine/threonine protein kinase


Mass: 444670.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S842
#2: Protein Spt20-like SEP domain-containing protein


Mass: 128449.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYM2
#3: Protein Uncharacterized protein


Mass: 48541.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S660
#10: Protein SCA7 domain-containing protein


Mass: 137082.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6A1
#11: Protein Putative transcription initiation factor


Mass: 28834.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)

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Transcription initiation factor TFIID subunit ... , 4 types, 4 molecules DEGI

#4: Protein Transcription initiation factor TFIID subunit 5


Mass: 83784.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SH10
#5: Protein Transcription initiation factor TFIID subunit 6 / TBP-associated factor 6


Mass: 52463.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S770
#6: Protein Transcription initiation factor TFIID subunit 10


Mass: 21417.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYR4
#8: Protein Transcription initiation factor TFIID subunit 12


Mass: 83091.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S2A1

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Putative transcriptional ... , 2 types, 2 molecules HK

#7: Protein Putative transcriptional coactivator HFI1 protein


Mass: 52133.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SED0
#9: Protein Putative transcriptional activator protein


Mass: 150297.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)

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Details

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: Core module of ctSAGA complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
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: OTHER
Electron lensMode: OTHER / 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
5CTFFINDCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1734991 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002421609
ELECTRON MICROSCOPYf_angle_d0.468929242
ELECTRON MICROSCOPYf_chiral_restr0.03733212
ELECTRON MICROSCOPYf_plane_restr0.00433827
ELECTRON MICROSCOPYf_dihedral_angle_d4.82052936

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