+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11712 | |||||||||
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Title | HDAC-DC-nucleosome | |||||||||
Map data | HDAC-DC-nucleosome | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / unidentified plasmid (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.6 Å | |||||||||
Authors | Lee J-H / Bollschweiler D / Schaefer T / Huber R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies. Authors: Jung-Hoon Lee / Daniel Bollschweiler / Tillman Schäfer / Robert Huber / Abstract: The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup ...The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification. | |||||||||
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_11712.map.gz | 31.8 MB | EMDB map data format | |
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Header (meta data) | emd-11712-v30.xml emd-11712.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_11712.png | 49.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11712 | HTTPS FTP |
-Validation report
Summary document | emd_11712_validation.pdf.gz | 220.9 KB | Display | EMDB validaton report |
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Full document | emd_11712_full_validation.pdf.gz | 220.1 KB | Display | |
Data in XML | emd_11712_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11712 | HTTPS FTP |
-Related 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_11712.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HDAC-DC-nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.885 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 : HDAC-PC-Nuc
Entire | Name: HDAC-PC-Nuc |
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Components |
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-Supramolecule #1: HDAC-PC-Nuc
Supramolecule | Name: HDAC-PC-Nuc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14 |
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-Supramolecule #2: Histone deacetylase
Supramolecule | Name: Histone deacetylase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Histone
Supramolecule | Name: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#12 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #4: DNA
Supramolecule | Name: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #13-#14 |
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Source (natural) | Organism: unidentified plasmid (others) |
Recombinant expression | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.8 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 9534 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Details | Real space refinement |
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