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- PDB-6z6p: HDAC-PC-Nuc -

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Basic information

Entry
Database: PDB / ID: 6z6p
TitleHDAC-PC-Nuc
Components
  • (DNA (145-MER)) x 2
  • (HDA1 complex subunit ...) x 2
  • (Histone H2B) x 2
  • (Histone H4) x 2
  • (Histone deacetylase ...) x 2
  • Histone H2A
  • Histone H2A type 1
  • Histone H3
  • Histone H3.2
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 / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / 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 / cytosol
Similarity search - Function
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 family / Histone deacetylase domain ...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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H2B / Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone deacetylase HDA1 / Histone H4 ...DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H2B / Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone deacetylase HDA1 / Histone H4 / Histone H3.2 / HDA1 complex subunit 3 / HDA1 complex subunit 2 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
unidentified plasmid (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 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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Structure viewerMolecule:
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Assembly

Deposited unit
K: Histone deacetylase HDA1
L: Histone deacetylase HDA1
M: HDA1 complex subunit 3,HDA1 complex subunit 3
N: HDA1 complex subunit 2
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,63516
Polymers460,50414
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Histone deacetylase ... , 2 types, 2 molecules KL

#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

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HDA1 complex subunit ... , 2 types, 2 molecules MN

#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

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Protein , 8 types, 8 molecules ABCDEFGH

#5: Protein Histone H3


Mass: 11431.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1, UniProt: P84233*PLUS
#6: Protein Histone H4


Mass: 9409.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#7: Protein Histone H2A


Mass: 11294.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, h2ac14, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#8: Protein Histone H2B


Mass: 10607.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18032685mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L8FQA5, UniProt: P02281*PLUS
#9: Protein Histone H3.2


Mass: 11405.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#10: Protein Histone H4


Mass: 8795.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#11: Protein Histone H2A type 1


Mass: 11494.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#12: Protein Histone H2B


Mass: 10348.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18032686mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L8FQ56, UniProt: P02281*PLUS

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DNA chain , 2 types, 2 molecules IJ

#13: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified plasmid (others)
#14: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified plasmid (others)

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Non-polymers , 1 types, 2 molecules

#15: Chemical ChemComp-ZN / ZINC ION


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

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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1HDAC-PC-NucCOMPLEX#1-#140RECOMBINANT
2Histone deacetylaseCOMPLEX#1-#41RECOMBINANT
3HistoneCOMPLEX#5-#121RECOMBINANT
4DNACOMPLEX#13-#141RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
33Xenopus laevis (African clawed frog)8355
44unidentified plasmid (others)45202
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
44synthetic construct (others)32630
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 77.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
9PHENIXmodel refinement
13cisTEM13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41279 / 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: 407.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009632302
ELECTRON MICROSCOPYf_angle_d1.605944900
ELECTRON MICROSCOPYf_chiral_restr0.08745058
ELECTRON MICROSCOPYf_plane_restr0.01074730
ELECTRON MICROSCOPYf_dihedral_angle_d25.060112645

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