+Open data
-Basic information
Entry | Database: PDB / ID: 6t9k | |||||||||
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Title | SAGA Core module | |||||||||
Components |
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Keywords | GENE 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 / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex ...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 / RNA polymerase II transcribes snRNA genes / 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 general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / IRE1-mediated unfolded protein response / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ub-specific processing proteases / mRNA export from nucleus / RNA polymerase II preinitiation complex assembly / enzyme activator activity / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / transcription coregulator activity / peroxisome / chromatin organization / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / molecular adaptor activity / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / 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 | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wang, H. / Cheung, A. / Cramer, P. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6t9k.cif.gz | 502.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9k.ent.gz | 368.6 KB | Display | PDB format |
PDBx/mmJSON format | 6t9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t9k_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6t9k_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6t9k_validation.xml.gz | 78.3 KB | Display | |
Data in CIF | 6t9k_validation.cif.gz | 119.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9k ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9k | HTTPS FTP |
-Related structure data
Related structure data | 10414MC 6t9iC 6t9jC 6t9lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 4 types, 4 molecules BCQU
#1: Protein | 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 |
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#2: Protein | 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 | 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 | Mass: 11035.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) |
-Transcription initiation factor TFIID subunit ... , 5 types, 5 molecules DEFGI
#3: Protein | 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 |
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#4: Protein | 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 | 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 | 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 | 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 |
-Transcriptional ... , 2 types, 2 molecules HK
#7: Protein | 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 |
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#9: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SAGA Core module / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) | ||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae S288C (yeast) | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: Solution were made from stock solution | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 4 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 42.45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 250368 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27602 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 107.1 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |