6Z6P

HDAC-PC-Nuc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.43 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. 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase HDA1A [auth K]661Saccharomyces 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53973
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase HDA1B [auth L]672Saccharomyces 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53973
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HDA1 complex subunit 3,HDA1 complex subunit 3C [auth M]543Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA3PLO1YPR179C
UniProt
Find proteins for Q06623 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06623 
Go to UniProtKB:  Q06623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06623
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HDA1 complex subunit 2D [auth N]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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06629
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3E [auth A]97Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84233
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth B]83Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62799
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AG [auth C]103Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajh2ac14LOC494591XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
Explore Q6AZJ8 
Go to UniProtKB:  Q6AZJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6AZJ8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BH [auth D]95Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032685mg
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02281
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2I [auth E]97Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84233
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4J [auth F]78Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62799
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1K [auth G]105Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06897
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BL [auth H]93Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02281
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (145-MER)M [auth I]145unidentified plasmid
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (145-MER)N [auth J]145unidentified plasmid
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcisTEM1

Structure Validation

View Full Validation Report



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