+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10412 | |||||||||
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Title | cryo-EM structure of transcription coactivator SAGA | |||||||||
Map data | ||||||||||
Sample |
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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 | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang H / Cheung A / Cramer P | |||||||||
Funding support | Germany, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10412.map.gz | 222.7 MB | EMDB map data format | |
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Header (meta data) | emd-10412-v30.xml emd-10412.xml | 30.5 KB 30.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10412_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10412.png | 135.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10412 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10412 | HTTPS FTP |
-Related structure data
Related structure data | 6t9iMC 6t9jC 6t9kC 6t9lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10412.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : SAGA complex
+Supramolecule #1: SAGA complex
+Macromolecule #1: Transcription factor SPT20
+Macromolecule #2: Protein SPT3
+Macromolecule #3: Transcription initiation factor TFIID subunit 5
+Macromolecule #4: Transcription initiation factor TFIID subunit 6
+Macromolecule #5: Transcription initiation factor TFIID subunit 9
+Macromolecule #6: Transcription initiation factor TFIID subunit 10
+Macromolecule #7: Transcriptional coactivator HFI1/ADA1
+Macromolecule #8: Transcription initiation factor TFIID subunit 12
+Macromolecule #9: Transcriptional activator SPT7
+Macromolecule #10: SAGA-associated factor 73
+Macromolecule #11: Transcription-associated protein 1
+Macromolecule #12: unassigned sequence
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solution were made from stock solution | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 42.45 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient |
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Output model | PDB-6t9i: |