6Z6F

HDAC-PC

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.

Lee, J.H., Bollschweiler, D., Schafer, T., Huber, R.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd4413
  • Primary Citation of Related Structures:  
    6Z6F, 6Z6H, 6Z6O, 6Z6P

  • PubMed 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 and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive ...

    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 2 -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.

    Organizational Affiliation: 

    Fakultät für Chemie, Technische Universität München, 85747 Garching, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase HDA1A661Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1, YNL021W, N2819
EC: 3.5.1.98
UniProt
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Go to UniProtKB:  P53973
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UniProt GroupP53973
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase HDA1B672Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1, YNL021W, N2819
EC: 3.5.1.98
UniProt
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Go to UniProtKB:  P53973
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UniProt GroupP53973
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HDA1 complex subunit 3,HDA1 complex subunit 3C [auth D]543Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA3, PLO1, YPR179C
UniProt
Find proteins for Q06623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ06623
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HDA1 complex subunit 2D [auth C]629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA2, PLO2, YDR295C
UniProt
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Go to UniProtKB:  Q06629
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UniProt GroupQ06629
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release