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- PDB-6t9i: cryo-EM structure of transcription coactivator SAGA -

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Basic information

Entry
Database: PDB / ID: 6t9i
Titlecryo-EM structure of transcription coactivator SAGA
Components
  • (Transcription initiation factor TFIID subunit ...) x 5
  • (Transcriptional ...Transcription (biology)) x 2
  • Protein SPT3
  • SAGA-associated factor 73
  • Transcription factor SPT20SPT20
  • Transcription-associated protein 1
  • unassigned sequence
KeywordsGENE REGULATION / Coactivator / Transcription / Histone acetyltransferase / Histone deubiquitinase
Function / homology
Function and homology information


RITS complex assembly / conjugation with cellular fusion / DUBm complex / pseudohyphal growth / : / : / positive regulation of DNA-templated transcription initiation / : / invasive growth in response to glucose limitation / regulation of nucleocytoplasmic transport ...RITS complex assembly / conjugation with cellular fusion / DUBm complex / pseudohyphal growth / : / : / positive regulation of DNA-templated transcription initiation / : / invasive growth in response to glucose limitation / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / NuA4 histone acetyltransferase complex / RNA polymerase II transcribes snRNA genes / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / IRE1-mediated unfolded protein response / enzyme activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / ubiquitin binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / chromatin organization / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / 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 / mitochondrion / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcriptional activator Spt7 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA-associated factor 73 / SCA7 domain ...Transcriptional activator Spt7 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA-associated factor 73 / SCA7 domain / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / SCA7, zinc-binding domain / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / SCA7 domain profile. / LisH / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat 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 / PIK-related kinase, FAT / FAT domain / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein SPT3 / Transcriptional activator SPT7 / Transcription initiation factor TFIID subunit 5 / Transcription-associated protein 1 / Transcription factor SPT20 / Transcription initiation factor TFIID subunit 6 / SAGA-associated factor 73 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 10 / Transcriptional coactivator HFI1/ADA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang, H. / Cheung, A. / Cramer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB860, SPP1935, EXC 2067/1-390729940 Germany
European Research Council693023 Germany
CitationJournal: Nature / Year: 2020
Title: Structure of the transcription coactivator SAGA.
Authors: Haibo Wang / Christian Dienemann / Alexandra Stützer / Henning Urlaub / Alan C M Cheung / Patrick Cramer /
Abstract: Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is ...Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is required for all regulated transcription and is conserved among eukaryotes. SAGA contains four modules: the activator-binding Tra1 module, the core module, the histone acetyltransferase (HAT) module and the histone deubiquitination (DUB) module. Previous studies provided partial structures, but the structure of the central core module is unknown. Here we present the cryo-electron microscopy structure of SAGA from the yeast Saccharomyces cerevisiae and resolve the core module at 3.3 Å resolution. The core module consists of subunits Taf5, Sgf73 and Spt20, and a histone octamer-like fold. The octamer-like fold comprises the heterodimers Taf6-Taf9, Taf10-Spt7 and Taf12-Ada1, and two histone-fold domains in Spt3. Spt3 and the adjacent subunit Spt8 interact with the TATA box-binding protein (TBP). The octamer-like fold and its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt distinct conformations. Taf12 and Spt20 form flexible connections to the Tra1 module, whereas Sgf73 tethers the DUB module. Binding of a nucleosome to SAGA displaces the HAT and DUB modules from the core-module surface, allowing the DUB module to bind one face of an ubiquitinated nucleosome.
History
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
B: Transcription factor SPT20
C: Protein SPT3
D: Transcription initiation factor TFIID subunit 5
E: Transcription initiation factor TFIID subunit 6
F: Transcription initiation factor TFIID subunit 9
G: Transcription initiation factor TFIID subunit 10
H: Transcriptional coactivator HFI1/ADA1
I: Transcription initiation factor TFIID subunit 12
K: Transcriptional activator SPT7
Q: SAGA-associated factor 73
T: Transcription-associated protein 1
U: unassigned sequence


Theoretical massNumber of molelcules
Total (without water)1,080,34512
Polymers1,080,34512
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area91140 Å2
ΔGint-511 kcal/mol
Surface area254760 Å2
MethodPISA

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Components

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Protein , 5 types, 5 molecules BCQTU

#1: Protein Transcription factor SPT20 / SPT20


Mass: 67880.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P50875
#2: Protein Protein SPT3 / Positive regulator of Ty transcription


Mass: 38864.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06844
#10: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 72976.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53165
#11: Protein Transcription-associated protein 1 / p400 kDa component of SAGA


Mass: 433677.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38811
#12: Protein unassigned sequence


Mass: 11035.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

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Transcription initiation factor TFIID subunit ... , 5 types, 5 molecules DEFGI

#3: Protein Transcription initiation factor TFIID subunit 5 / TAFII-90 / TBP-associated factor 5 / TBP-associated factor 90 kDa


Mass: 89081.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38129
#4: Protein Transcription initiation factor TFIID subunit 6 / TBP-associated factor 6 / TBP-associated factor 60 kDa / TAFII60


Mass: 57964.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53040
#5: Protein Transcription initiation factor TFIID subunit 9 / TAFII-17 / TAFII20 / TBP-associated factor 17 kDa / TBP-associated factor 9


Mass: 17334.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05027
#6: Protein Transcription initiation factor TFIID subunit 10 / TAFII-23 / TAFII23 / TAFII-25 / TAFII25 / TBP-associated factor 10 / TBP-associated factor 25 kDa / p25


Mass: 23042.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12030
#8: Protein Transcription initiation factor TFIID subunit 12 / TAFII-61 / TAFII61 / TAFII-68 / TAFII68 / TBP-associated factor 12 / TBP-associated factor 61 kDa


Mass: 61144.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03761

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Transcriptional ... , 2 types, 2 molecules HK

#7: Protein Transcriptional coactivator HFI1/ADA1


Mass: 54529.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12060
#9: Protein Transcriptional activator SPT7


Mass: 152813.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35177

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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: SAGA complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.5 / Details: Solution were made from stock solution
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaClSodium chloride1
31 mMDithiothreitolC4H10O2S21
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 42.45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4Warp1.0.6CTF correction
7Coot0.8.9model fitting
10RELION3.0.5final Euler assignment
12RELION3.0.53D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 250368
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27602 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

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