+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2693 | |||||||||
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Title | MAPPING THE DEUBIQUITINATION MODULE WITHIN THE SAGA COMPLEX | |||||||||
Map data | Structure of the yeast (S. cerevisiae) SAGA complex | |||||||||
Sample |
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Keywords | SAGA / Eukaryotic Transcription / Deubiquitination module | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.3 Å | |||||||||
Authors | Durand A / Bonnet J / Fournier M / Schultz P | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Mapping the deubiquitination module within the SAGA complex. Abstract: The molecular organization of the yeast transcriptional coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA) was analyzed by single-particle electron microscopy. Complete or partial deletion of the ...The molecular organization of the yeast transcriptional coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA) was analyzed by single-particle electron microscopy. Complete or partial deletion of the Sgf73 subunit disconnects the deubiquitination (DUB) module from SAGA and favors in our conditions the cleavage of the C-terminal ends of the Spt7 subunit and the loss of the Spt8 subunit. The structural comparison of the wild-type SAGA with two deletion mutants positioned the DUB module and enabled the fitting of the available atomic models. The localization of the DUB module close to Gcn5 defines a chromatin-binding interface within SAGA, which could be demonstrated by the binding of nucleosome core particles. The TATA-box binding protein (TBP)-interacting subunit Spt8 was found to be located close to the DUB but in a different domain than Spt3, also known to contact TBP. A flexible protein arm brings both subunits close enough to interact simultaneously with TBP. | |||||||||
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_2693.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-2693-v30.xml emd-2693.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | EMD-2693-12628.png | 100.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2693 | HTTPS FTP |
-Validation report
Summary document | emd_2693_validation.pdf.gz | 185 KB | Display | EMDB validaton report |
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Full document | emd_2693_full_validation.pdf.gz | 184.2 KB | Display | |
Data in XML | emd_2693_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2693 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2693.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the yeast (S. cerevisiae) SAGA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 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 : S. cerevisiae SAGA complex
Entire | Name: S. cerevisiae SAGA complex |
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Components |
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-Supramolecule #1000: S. cerevisiae SAGA complex
Supramolecule | Name: S. cerevisiae SAGA complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1 |
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Molecular weight | Theoretical: 1.8 MDa |
-Macromolecule #1: SAGA
Macromolecule | Name: SAGA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4742 / synonym: Baker's yeast / Location in cell: Nuclear |
Molecular weight | Theoretical: 1.8 MDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 / Details: 500 mM NaCl, 30 mM Hepes, 2 mM EGTA |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein stained with 2% w/v uranyl acetate |
Grid | Details: 300 mesh Cu/Rh grid with glow discharge |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Oct 10, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 53846 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | IMAGIC |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.3 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 19226 |
Final two d classification | Number classes: 500 |