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- PDB-9ynw: Tra1, Core and minimal HAT modules of ctSAGA, composite. -

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Basic information

Entry
Database: PDB / ID: 9ynw
TitleTra1, Core and minimal HAT modules of ctSAGA, composite.
Components
  • (Putative transcriptional ...) x 2
  • (Transcription initiation factor TFIID subunit ...) x 4
  • (Uncharacterized ...) x 2
  • Non-specific serine/threonine protein kinase
  • Putative transcription initiation factor
  • SCA7 domain-containing protein
  • Spt20-like SEP domain-containing protein
  • Transcriptional adapter 2
  • histone acetyltransferase
KeywordsTRANSCRIPTION / ctSAGA complex / Histone Acetyl Transferase (HAT) Module / Tra1 module and Core module
Function / homology
Function and homology information


SAGA-type complex / RITS complex assembly / regulatory ncRNA-mediated heterochromatin formation / SLIK (SAGA-like) complex / histone H3 acetyltransferase activity / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / NuA4 histone acetyltransferase complex / histone acetyltransferase complex ...SAGA-type complex / RITS complex assembly / regulatory ncRNA-mediated heterochromatin formation / SLIK (SAGA-like) complex / histone H3 acetyltransferase activity / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / histone acetyltransferase / 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 / chromatin remodeling / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional activator Spt7 / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 ...Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional activator Spt7 / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / 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 / Histone acetyltransferase GCN5 / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Bromodomain associated / Bromodomain associated domain / 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 / Myb-like domain profile. / Lissencephaly type-1-like homology motif / SWIRM domain / SWIRM domain / SWIRM domain profile. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / FATC domain / PIK-related kinase, FAT / FAT domain / Myb-type HTH DNA-binding domain profile. / SANT domain profile. / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC 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 / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / GNAT domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / SANT/Myb domain / Acyl-CoA N-acyltransferase / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / 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 / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Spt20-like SEP domain-containing protein / Transcription initiation factor TFIID subunit 10 / SAGA complex subunit Spt7 / Transcription initiation factor TFIID subunit 12 domain-containing protein / Uncharacterized protein / SCA7 domain-containing protein / TBP-associated factor 6 / Transcriptional adapter 2 / Non-specific serine/threonine protein kinase / histone acetyltransferase ...Spt20-like SEP domain-containing protein / Transcription initiation factor TFIID subunit 10 / SAGA complex subunit Spt7 / Transcription initiation factor TFIID subunit 12 domain-containing protein / Uncharacterized protein / SCA7 domain-containing protein / TBP-associated factor 6 / Transcriptional adapter 2 / Non-specific serine/threonine protein kinase / histone acetyltransferase / Uncharacterized protein / 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: 3.5 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 12, 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

Downloads & links

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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
F: Putative transcription initiation factor
G: Transcription initiation factor TFIID subunit 10
I: Transcription initiation factor TFIID subunit 12
K: Putative transcriptional activator protein
Q: SCA7 domain-containing protein
H: Putative transcriptional coactivator HFI1 protein
M: Transcriptional adapter 2
N: histone acetyltransferase
O: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)1,398,04614
Polymers1,398,04614
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 , 6 types, 6 molecules ABFQMN

#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
#6: 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)
#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
#12: 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
#13: 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

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Uncharacterized ... , 2 types, 2 molecules CO

#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
#14: Protein Uncharacterized protein


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

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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
#7: 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 KH

#9: Protein Putative transcriptional activator protein


Mass: 131755.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S267
#11: 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

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Details

Has protein modificationY

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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: Tra1 module of ctSAGA complex / Type: COMPLEX / Entity ID: #10, #2-#6 / 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
1EMANparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 3566416 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 80.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002162208
ELECTRON MICROSCOPYf_angle_d0.462484225
ELECTRON MICROSCOPYf_chiral_restr0.03659303
ELECTRON MICROSCOPYf_plane_restr0.004410943
ELECTRON MICROSCOPYf_dihedral_angle_d4.37388315

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