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- PDB-8bpa: Cryo-EM structure of the human SIN3B histone deacetylase complex ... -

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Basic information

Entry
Database: PDB / ID: 8bpa
TitleCryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom
Components
  • Histone deacetylase 2
  • Isoform 2 of Paired amphipathic helix protein Sin3b
  • Mortality factor 4-like protein 1
  • PHD finger protein 12
KeywordsGENE REGULATION / HDAC / Chromatin / Cell cycle / transcription
Function / homology
Function and homology information


autosome / positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / fungiform papilla formation / epidermal cell differentiation / histone decrotonylase activity / negative regulation of transcription initiation by RNA polymerase II ...autosome / positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / fungiform papilla formation / epidermal cell differentiation / histone decrotonylase activity / negative regulation of transcription initiation by RNA polymerase II / NuRD complex / positive regulation of interleukin-1 production / : / regulation of cell fate specification / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of stem cell population maintenance / regulation of stem cell differentiation / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / ESC/E(Z) complex / cardiac muscle hypertrophy / cellular response to dopamine / positive regulation of intracellular estrogen receptor signaling pathway / behavioral response to ethanol / STAT3 nuclear events downstream of ALK signaling / odontogenesis of dentin-containing tooth / XY body / regulation of double-strand break repair / embryonic digit morphogenesis / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / response to caffeine / eyelid development in camera-type eye / Notch-HLH transcription pathway / Y chromosome / positive regulation of oligodendrocyte differentiation / Sin3-type complex / X chromosome / positive regulation of stem cell population maintenance / dendrite development / histone deacetylase complex / NuA4 histone acetyltransferase complex / response to amyloid-beta / positive regulation of proteolysis / progesterone receptor signaling pathway / RNA Polymerase I Transcription Initiation / hair follicle placode formation / response to hyperoxia / Regulation of MECP2 expression and activity / cellular response to transforming growth factor beta stimulus / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / NF-kappaB binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to retinoic acid / positive regulation of double-strand break repair via homologous recombination / Regulation of TP53 Activity through Acetylation / transcription repressor complex / MECP2 regulates neuronal receptors and channels / Regulation of lipid metabolism by PPARalpha / heat shock protein binding / phosphatidylinositol binding / response to amphetamine / negative regulation of cell migration / transcription corepressor binding / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / transcription coregulator binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to nicotine / Regulation of endogenous retroelements by KRAB-ZFP proteins / circadian regulation of gene expression / response to cocaine / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / Cytoprotection by HMOX1 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / double-strand break repair via homologous recombination / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to hydrogen peroxide / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of tumor necrosis factor production / transcription corepressor activity / nucleosome / negative regulation of neuron projection development / cellular response to heat / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / response to lipopolysaccharide / chromatin organization / heterochromatin formation / histone binding / regulation of apoptotic process
Similarity search - Function
PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 / PHD finger protein 12 MRG binding domain / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting ...PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 / PHD finger protein 12 MRG binding domain / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / MRG / MRG domain / Paired amphipathic helix superfamily / MRG, C-terminal domain superfamily / Paired amphipathic helix repeat / MRG / PAH domain profile. / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Histone deacetylase / Forkhead-associated (FHA) domain profile. / Forkhead-associated (FHA) domain / Chromo-like domain superfamily / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / SMAD/FHA domain superfamily / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Paired amphipathic helix protein Sin3b / Histone deacetylase 2 / PHD finger protein 12 / Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWan, M.S.M. / Muhammad, R. / Koliopolous, M.G. / Alfieri, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215458/Z/19/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
Authors: Mandy S M Wan / Reyhan Muhammad / Marios G Koliopoulos / Theodoros I Roumeliotis / Jyoti S Choudhary / Claudio Alfieri /
Abstract: Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing ...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.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Paired amphipathic helix protein Sin3b
B: Histone deacetylase 2
C: PHD finger protein 12
D: Mortality factor 4-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,78011
Polymers336,3724
Non-polymers4077
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Isoform 2 of Paired amphipathic helix protein Sin3b / Histone deacetylase complex subunit Sin3b / Transcriptional corepressor Sin3b


Mass: 129547.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIN3B, KIAA0700 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75182
#2: Protein Histone deacetylase 2 / HD2 / Protein deacylase HDAC2


Mass: 55443.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q92769, histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Protein PHD finger protein 12 / PHD factor 1 / Pf1


Mass: 109841.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF12, KIAA1523 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96QT6
#4: Protein Mortality factor 4-like protein 1 / MORF-related gene 15 protein / Protein MSL3-1 / Transcription factor-like protein MRG15


Mass: 41540.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UBU8

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Non-polymers , 2 types, 7 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SIN3B core complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49835 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510627
ELECTRON MICROSCOPYf_angle_d0.8214352
ELECTRON MICROSCOPYf_dihedral_angle_d4.8741408
ELECTRON MICROSCOPYf_chiral_restr0.0461534
ELECTRON MICROSCOPYf_plane_restr0.0061862

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