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- PDB-8c60: Cryo-EM structure of the human SIN3B full-length complex at 3.4 A... -

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Basic information

Entry
Database: PDB / ID: 8c60
TitleCryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution
Components
  • Histone deacetylase 2
  • Isoform 2 of Paired amphipathic helix protein Sin3b
  • Mortality factor 4-like protein 1
  • PHD finger protein 12
KeywordsHYDROLASE / Chromatin / Histone deacetylase / HDAC
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 / eyelid development in camera-type eye / histone decrotonylase activity ...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 / eyelid development in camera-type eye / 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 / positive regulation of intracellular estrogen receptor signaling pathway / behavioral response to ethanol / odontogenesis of dentin-containing tooth / STAT3 nuclear events downstream of ALK signaling / cellular response to dopamine / XY body / embryonic digit morphogenesis / regulation of double-strand break repair / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / response to caffeine / Notch-HLH transcription pathway / Y chromosome / positive regulation of oligodendrocyte differentiation / X chromosome / Sin3-type complex / dendrite development / positive regulation of stem cell population maintenance / transcription repressor complex / histone deacetylase complex / response to amyloid-beta / progesterone receptor signaling pathway / NuA4 histone acetyltransferase complex / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / hair follicle placode formation / response to hyperoxia / cellular response to transforming growth factor beta stimulus / Regulation of MECP2 expression and activity / 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 / Regulation of TP53 Activity through Acetylation / positive regulation of double-strand break repair via homologous recombination / MECP2 regulates neuronal receptors and channels / Regulation of lipid metabolism by PPARalpha / heat shock protein binding / response to amphetamine / phosphatidylinositol binding / negative regulation of cell migration / regulation of embryonic development / negative regulation of transforming growth factor beta receptor signaling pathway / transcription corepressor binding / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of chromatin organization proteins / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to nicotine / circadian regulation of gene expression / response to cocaine / Regulation of endogenous retroelements by KRAB-ZFP proteins / negative regulation of neuron projection development / HDACs deacetylate histones / Cytoprotection by HMOX1 / promoter-specific chromatin binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / cellular response to hydrogen peroxide / NOTCH1 Intracellular Domain Regulates Transcription / 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 / cellular response to heat / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / response to lipopolysaccharide / heterochromatin formation / histone binding / chromatin organization
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 / Histone deacetylase domain / Forkhead-associated (FHA) domain profile. / Forkhead-associated (FHA) domain / Arginase; Chain A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
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: 3.4 Å
AuthorsAlfieri, C. / Wan, S.M. / Muhammad, R.
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
DepositionJan 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
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Revision 1.1May 17, 2023Group: Database references / Category: citation
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Revision 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
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Revision 1.1Jul 2, 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: gel filtration
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 (butterflies/moths) / 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: Human SIN3B complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.385 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38352 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410627
ELECTRON MICROSCOPYf_angle_d0.74214352
ELECTRON MICROSCOPYf_dihedral_angle_d4.4991408
ELECTRON MICROSCOPYf_chiral_restr0.0461534
ELECTRON MICROSCOPYf_plane_restr0.0061862

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