8BPA

Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.

Wan, M.S.M.Muhammad, R.Koliopoulos, M.G.Roumeliotis, T.I.Choudhary, J.S.Alfieri, C.

(2023) Nat Commun 14: 2556-2556

  • DOI: https://doi.org/10.1038/s41467-023-38276-0
  • Primary Citation of Related Structures:  
    8BPA, 8BPB, 8BPC, 8C60

  • PubMed Abstract: 

    Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.


  • Organizational Affiliation

    Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Paired amphipathic helix protein Sin3b1,130Homo sapiensMutation(s): 0 
Gene Names: SIN3BKIAA0700
UniProt & NIH Common Fund Data Resources
Find proteins for O75182 (Homo sapiens)
Explore O75182 
Go to UniProtKB:  O75182
PHAROS:  O75182
GTEx:  ENSG00000127511 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75182
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 2488Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens)
Explore Q92769 
Go to UniProtKB:  Q92769
PHAROS:  Q92769
GTEx:  ENSG00000196591 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92769
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 121,004Homo sapiensMutation(s): 0 
Gene Names: PHF12KIAA1523
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QT6 (Homo sapiens)
Explore Q96QT6 
Go to UniProtKB:  Q96QT6
PHAROS:  Q96QT6
GTEx:  ENSG00000109118 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QT6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mortality factor 4-like protein 1362Homo sapiensMutation(s): 0 
Gene Names: MORF4L1MRG15FWP006HSPC008HSPC061PP368
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBU8 (Homo sapiens)
Explore Q9UBU8 
Go to UniProtKB:  Q9UBU8
PHAROS:  Q9UBU8
GTEx:  ENSG00000185787 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBU8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom215458/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references