8BPA | pdb_00008bpa

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

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 336.78 kDa 
  • Atom Count: 10,393 
  • Modeled Residue Count: 1,280 
  • Deposited Residue Count: 2,984 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  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
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UniProt GroupO75182
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Reference Sequence
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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 
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UniProt GroupQ92769
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Reference Sequence
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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 
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UniProt GroupQ96QT6
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Reference Sequence
Find similar proteins by:|  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 
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UniProt GroupQ9UBU8
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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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
  • Version 1.2: 2025-07-09
    Changes: Data collection, Structure summary