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


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

  • 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 HDA1A [auth K]661Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1YNL021WN2819
EC: 3.5.1.98
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase HDA1B [auth L]672Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA1YNL021WN2819
EC: 3.5.1.98
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HDA1 complex subunit 3,HDA1 complex subunit 3C [auth M]543Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA3PLO1YPR179C
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HDA1 complex subunit 2D [auth N]629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HDA2PLO2YDR295C
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3E [auth A]97Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F [auth B]83Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AG [auth C]103Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajh2ac14LOC494591XELAEV_18003602mgh2ac14.L
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BH [auth D]95Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032685mg
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2I [auth E]97Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4J [auth F]78Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1K [auth G]105Xenopus laevisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BL [auth H]93Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
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Entity ID: 13
MoleculeChainsLengthOrganismImage
DNA (145-MER)M [auth I]145unidentified plasmid
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (145-MER)N [auth J]145unidentified plasmid
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
O [auth K], P [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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