+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10415 | |||||||||
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Title | SAGA DUB module bound to a ubiqitinated nucleosome | |||||||||
Map data | postprocess masked map | |||||||||
Sample |
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Keywords | Coactivator / Transcription / Histone acetyltransferase / Histone deubiquitinase / GENE REGULATION | |||||||||
Function / homology | Function and homology information RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ub-specific processing proteases / mRNA export from nucleus / nuclear pore / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / enzyme activator activity / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / RNA splicing / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Hh mutants are degraded by ERAD Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang H / 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_10415.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-10415-v30.xml emd-10415.xml | 33.9 KB 33.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10415_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_10415.png | 150.7 KB | ||
Filedesc metadata | emd-10415.cif.gz | 8.3 KB | ||
Others | emd_10415_half_map_1.map.gz emd_10415_half_map_2.map.gz | 193.9 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10415 | HTTPS FTP |
-Validation report
Summary document | emd_10415_validation.pdf.gz | 608.4 KB | Display | EMDB validaton report |
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Full document | emd_10415_full_validation.pdf.gz | 322.9 KB | Display | |
Data in XML | emd_10415_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_10415_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10415 | HTTPS FTP |
-Related structure data
Related structure data | 6t9lMC 6t9iC 6t9jC 6t9kC 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_10415.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocess masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_10415_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10415_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SAGA DUB-ubiqitinated nucleosome complex
+Supramolecule #1: SAGA DUB-ubiqitinated nucleosome complex
+Supramolecule #2: nucleosome
+Supramolecule #3: SAGA DUB module
+Supramolecule #4: DNA
+Supramolecule #5: Ubiquitin carboxyl-terminal hydrolase 8
+Supramolecule #6: ubiquitin
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #5: Histone H2B
+Macromolecule #8: Ubiquitin carboxyl-terminal hydrolase 8
+Macromolecule #9: Transcription and mRNA export factor SUS1
+Macromolecule #10: SAGA-associated factor 11
+Macromolecule #11: SAGA-associated factor 73
+Macromolecule #12: Polyubiquitin-C
+Macromolecule #6: Widom601 DNA (145-MER)
+Macromolecule #7: Widom601 DNA (145-MER)
+Macromolecule #13: ZINC ION
-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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 44.17 e/Å2 |
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 FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |