+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35458 | |||||||||
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Title | Rpd3S apo state 3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HDAC / TRANSCRIPTION | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.82 Å | |||||||||
Authors | Zhang Y | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Authors: Yueyue Zhang / Mengxue Xu / Po Wang / Jiahui Zhou / Guangxian Wang / Shuailong Han / Gang Cai / Xuejuan Wang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35458.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-35458-v30.xml emd-35458.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_35458.png | 34.3 KB | ||
Filedesc metadata | emd-35458.cif.gz | 3.5 KB | ||
Others | emd_35458_half_map_1.map.gz emd_35458_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35458 | HTTPS FTP |
-Validation report
Summary document | emd_35458_validation.pdf.gz | 691.4 KB | Display | EMDB validaton report |
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Full document | emd_35458_full_validation.pdf.gz | 691 KB | Display | |
Data in XML | emd_35458_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_35458_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35458 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35458 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35458.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35458_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35458_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rpd3S
Entire | Name: Rpd3S |
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Components |
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-Supramolecule #1: Rpd3S
Supramolecule | Name: Rpd3S / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23259 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |