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- PDB-6z6f: HDAC-PC -

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Basic information

Entry
Database: PDB / ID: 6z6f
TitleHDAC-PC
Components
  • (Histone deacetylase HDA1) x 2
  • HDA1 complex subunit 2
  • HDA1 complex subunit 3,HDA1 complex subunit 3
KeywordsGENE REGULATION / Protein complex
Function / homology
Function and homology information


HDA1 complex / : / HSF1 activation / HDACs deacetylate histones / nucleosome array spacer activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase complex ...HDA1 complex / : / HSF1 activation / HDACs deacetylate histones / nucleosome array spacer activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase complex / epigenetic regulation of gene expression / chromosome segregation / chromatin organization / 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 / identical protein binding / nucleus / cytosol
Similarity search - Function
Rossmann fold - #12360 / Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2-like domain / Class II histone deacetylase complex subunits 2 and 3 / Histone deacetylase domain / Arginase; Chain A ...Rossmann fold - #12360 / Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2-like domain / Class II histone deacetylase complex subunits 2 and 3 / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone deacetylase HDA1 / HDA1 complex subunit 3 / HDA1 complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsLee, J.-H. / Bollschweiler, D. / Schaefer, T. / Huber, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: 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
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Histone deacetylase HDA1
B: Histone deacetylase HDA1
D: HDA1 complex subunit 3,HDA1 complex subunit 3
C: HDA1 complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,3376
Polymers286,2074
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23320 Å2
ΔGint-178 kcal/mol
Surface area109420 Å2
MethodPISA

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Components

#1: Protein Histone deacetylase HDA1


Mass: 74851.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase
#2: Protein Histone deacetylase HDA1


Mass: 76017.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA1, YNL021W, N2819 / Production host: Escherichia coli (E. coli) / References: UniProt: P53973, histone deacetylase
#3: Protein HDA1 complex subunit 3,HDA1 complex subunit 3 / Histone deacetylase complex 1 subunit 3


Mass: 63422.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA3, PLO1, YPR179C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06623
#4: Protein HDA1 complex subunit 2 / Histone deacetylase complex 1 subunit 2


Mass: 71915.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HDA2, PLO2, YDR295C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06629
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HDAC-PC / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 62.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
12cryoSPARC23D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 466972 / Symmetry type: POINT
Atomic model buildingDetails: Real space refinement
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 136.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00619602
ELECTRON MICROSCOPYf_angle_d1.019626500
ELECTRON MICROSCOPYf_chiral_restr0.062961
ELECTRON MICROSCOPYf_plane_restr0.00683405
ELECTRON MICROSCOPYf_dihedral_angle_d19.69017413

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