+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35095 | |||||||||
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Title | Cryo-EM map of the SIN3L complex from S. pombe in Prw1 region | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Wang C / Guo Z / Zhan X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2023 Title: Two assembly modes for SIN3 histone deacetylase complexes. Authors: Chengcheng Wang / Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Xiechao Zhan / Abstract: The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes ...The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35095.map.gz | 139.1 MB | EMDB map data format | |
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Header (meta data) | emd-35095-v30.xml emd-35095.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_35095.png | 36 KB | ||
Others | emd_35095_half_map_1.map.gz emd_35095_half_map_2.map.gz | 140.6 MB 140.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35095 | HTTPS FTP |
-Validation report
Summary document | emd_35095_validation.pdf.gz | 591.8 KB | Display | EMDB validaton report |
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Full document | emd_35095_full_validation.pdf.gz | 591.4 KB | Display | |
Data in XML | emd_35095_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_35095_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35095 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35095.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35095_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35095_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The SIN3L complex
Entire | Name: The SIN3L complex |
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Components |
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-Supramolecule #1: The SIN3L complex
Supramolecule | Name: The SIN3L complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 K3 (6k x 4k) / 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 / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263273 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |