+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26792 | |||||||||
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Title | Transcription co-activator SAGA | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Vasyliuk D / Yip CK | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Sci Rep / Year: 2022 Title: Conformational landscape of the yeast SAGA complex as revealed by cryo-EM. Authors: Diana Vasyliuk / Joeseph Felt / Ellen D Zhong / Bonnie Berger / Joseph H Davis / Calvin K Yip / Abstract: Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by ...Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by recruiting TATA box binding protein (TBP) to DNA. The prototypical yeast Saccharomyces cerevisiae SAGA contains 19 subunits that are organized into Tra1, core, histone acetyltransferase, and deubiquitination modules. Recent cryo-electron microscopy studies have generated high-resolution structural information on the Tra1 and core modules of yeast SAGA. However, the two catalytical modules were poorly resolved due to conformational flexibility of the full assembly. Furthermore, the high sample requirement created a formidable barrier to further structural investigations of SAGA. Here, we report a workflow for isolating/stabilizing yeast SAGA and preparing cryo-EM specimens at low protein concentration using a graphene oxide support layer. With this procedure, we were able to determine a cryo-EM reconstruction of yeast SAGA at 3.1 Å resolution and examine its conformational landscape with the neural network-based algorithm cryoDRGN. Our analysis revealed that SAGA adopts a range of conformations with its HAT module and central core in different orientations relative to Tra1. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26792.map.gz | 175.6 MB | EMDB map data format | |
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Header (meta data) | emd-26792-v30.xml emd-26792.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26792_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_26792.png | 65.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26792 | HTTPS FTP |
-Validation report
Summary document | emd_26792_validation.pdf.gz | 467.3 KB | Display | EMDB validaton report |
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Full document | emd_26792_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | emd_26792_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_26792_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26792 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26792.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.332 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SAGA
Entire | Name: SAGA |
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Components |
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-Supramolecule #1: SAGA
Supramolecule | Name: SAGA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303a |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: EMS Lacey Carbon / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 2s blot time, -5 blot force.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | PNCC Krios 4 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 17955 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |