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Open data
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Basic information
Entry | Database: PDB / ID: 6z6p | ||||||
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Title | HDAC-PC-Nuc | ||||||
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![]() | GENE REGULATION / Protein complex | ||||||
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 | ![]() ![]() ![]() unidentified plasmid (others) | ||||||
Method | ELECTRON MICROSCOPY / 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 722 KB | Display | ![]() |
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PDB format | ![]() | 566.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 860.9 KB | Display | ![]() |
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Full document | ![]() | 925.8 KB | Display | |
Data in XML | ![]() | 90.4 KB | Display | |
Data in CIF | ![]() | 142.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11102MC ![]() 6z6fC ![]() 6z6hC ![]() 6z6oC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Histone deacetylase ... , 2 types, 2 molecules KL
#1: Protein | Mass: 74851.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HDA1, YNL021W, N2819 / Production host: ![]() ![]() |
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#2: Protein | Mass: 76017.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HDA1, YNL021W, N2819 / Production host: ![]() ![]() |
-HDA1 complex subunit ... , 2 types, 2 molecules MN
#3: Protein | Mass: 63422.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HDA3, PLO1, YPR179C / Production host: ![]() ![]() |
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#4: Protein | Mass: 71915.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HDA2, PLO2, YDR295C / Production host: ![]() ![]() |
-Protein , 8 types, 8 molecules ABCDEFGH
#5: Protein | Mass: 11431.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: Protein | Mass: 9409.056 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#7: Protein | Mass: 11294.136 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#8: Protein | Mass: 10607.212 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#9: Protein | Mass: 11405.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#10: Protein | Mass: 8795.306 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#11: Protein | Mass: 11494.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#12: Protein | Mass: 10348.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules IJ
#13: DNA chain | Mass: 44520.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified plasmid (others) |
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#14: DNA chain | Mass: 44991.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified plasmid (others) |
-Non-polymers , 1 types, 2 molecules ![](data/chem/img/ZN.gif)
#15: Chemical |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 77.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41279 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Details: Real space refinement | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 407.11 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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