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


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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. 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

    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. hlee@biochem.mpg.de huber@biochem.mpg.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase HDA1661Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1YNL021WN2819
EC: 3.5.1.98
UniProt
Find proteins for P53973 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53973
Entity Groups  
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UniProt GroupP53973
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase HDA1672Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1YNL021WN2819
EC: 3.5.1.98
UniProt
Find proteins for P53973 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53973 
Go to UniProtKB:  P53973
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UniProt GroupP53973
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HDA1 complex subunit 3,HDA1 complex subunit 3C [auth D]543Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA3PLO1YPR179C
UniProt
Find proteins for Q06623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q06623
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UniProt GroupQ06623
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HDA1 complex subunit 2D [auth C]629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA2PLO2YDR295C
UniProt
Find proteins for Q06629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06629 
Go to UniProtKB:  Q06629
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UniProt GroupQ06629
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  • Reference Sequence
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