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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11102 | |||||||||
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Title | HDAC-PC-Nuc | |||||||||
![]() | HDAC-PC-Nuc | |||||||||
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Function / homology | ![]() HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / regulatory ncRNA-mediated gene silencing / histone deacetylase / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / chromosome segregation ...HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / regulatory ncRNA-mediated gene silencing / histone deacetylase / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / chromosome segregation / structural constituent of chromatin / nucleosome / nucleosome assembly / cellular response to lipopolysaccharide / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.43 Å | |||||||||
![]() | Lee J-H / Bollschweiler D / Schaefer T / Huber R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 296.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.9 KB 28.9 KB | Display Display | ![]() |
Images | ![]() | 16.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 249.1 KB | Display | ![]() |
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Full document | ![]() | 248.2 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z6pMC ![]() 6z6fC ![]() 6z6hC ![]() 6z6oC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | HDAC-PC-Nuc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : HDAC-PC-Nuc
+Supramolecule #1: HDAC-PC-Nuc
+Supramolecule #2: Histone deacetylase
+Supramolecule #3: Histone
+Supramolecule #4: DNA
+Macromolecule #1: Histone deacetylase HDA1
+Macromolecule #2: Histone deacetylase HDA1
+Macromolecule #3: HDA1 complex subunit 3,HDA1 complex subunit 3
+Macromolecule #4: HDA1 complex subunit 2
+Macromolecule #5: Histone H3
+Macromolecule #6: Histone H4
+Macromolecule #7: Histone H2A
+Macromolecule #8: Histone H2B
+Macromolecule #9: Histone H3.2
+Macromolecule #10: Histone H4
+Macromolecule #11: Histone H2A type 1
+Macromolecule #12: Histone H2B
+Macromolecule #13: DNA (145-MER)
+Macromolecule #14: DNA (145-MER)
+Macromolecule #15: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 77.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 41279 |
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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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Output model | ![]() PDB-6z6p: |