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- EMDB-16147: Cryo-EM structure of the human SIN3B histone deacetylase complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16147
TitleCryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom
Map dataSIN3B complex 3.7 Angstrom
Sample
  • Complex: SIN3B core complex
    • Protein or peptide: Isoform 2 of Paired amphipathic helix protein Sin3b
    • Protein or peptide: Histone deacetylase 2
    • Protein or peptide: PHD finger protein 12
    • Protein or peptide: Mortality factor 4-like protein 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
KeywordsHDAC / Chromatin / Cell cycle / transcription / GENE REGULATION
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 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol ...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 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / 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 transcription by competitive promoter binding / negative regulation of stem cell population maintenance / histone deacetylase activity, hydrolytic mechanism / ESC/E(Z) complex / histone deacetylase / regulation of stem cell differentiation / XY body / cardiac muscle hypertrophy / cellular response to dopamine / STAT3 nuclear events downstream of ALK signaling / regulation of double-strand break repair / response to caffeine / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of intracellular estrogen receptor signaling pathway / Notch-HLH transcription pathway / Y chromosome / X chromosome / Sin3-type complex / NuA4 histone acetyltransferase complex / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of stem cell population maintenance / dendrite development / response to amyloid-beta / RNA Polymerase I Transcription Initiation / histone deacetylase complex / positive regulation of oligodendrocyte differentiation / positive regulation of proteolysis / Regulation of MECP2 expression and activity / progesterone receptor signaling pathway / hair follicle placode formation / response to hyperoxia / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / positive regulation of double-strand break repair via homologous recombination / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / cellular response to retinoic acid / heat shock protein binding / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / phosphatidylinositol binding / negative regulation of cell migration / response to amphetamine / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / response to nicotine / response to cocaine / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / double-strand break repair via homologous recombination / Cytoprotection by HMOX1 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / protein modification process / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / transcription corepressor activity / nucleosome / heterochromatin formation / negative regulation of neuron projection development / cellular response to heat / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / chromatin organization / fibroblast proliferation / regulation of apoptotic process / histone binding / response to lipopolysaccharide
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 / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWan MSM / Muhammad R / Koliopolous MG / Alfieri C
Funding support United Kingdom, 1 items
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, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16147.png

Downloads & links

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Map

FileDownload / File: emd_16147.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSIN3B complex 3.7 Angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 216 pix.
= 221.616 Å		1.03 Å/pix.
x 216 pix.
= 221.616 Å		1.03 Å/pix.
x 216 pix.
= 221.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.026 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.050232343 - 2.0387588
Average (Standard dev.)0.002489504 (±0.037328236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 221.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SIN3B complex 3.7 Angstrom half2

Fileemd_16147_half_map_1.map
AnnotationSIN3B complex 3.7 Angstrom half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SIN3B complex 3.7 Angstrom half1

Fileemd_16147_half_map_2.map
AnnotationSIN3B complex 3.7 Angstrom half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SIN3B core complex

EntireName: SIN3B core complex
Components
  • Complex: SIN3B core complex
    • Protein or peptide: Isoform 2 of Paired amphipathic helix protein Sin3b
    • Protein or peptide: Histone deacetylase 2
    • Protein or peptide: PHD finger protein 12
    • Protein or peptide: Mortality factor 4-like protein 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: SIN3B core complex

SupramoleculeName: SIN3B core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Isoform 2 of Paired amphipathic helix protein Sin3b

MacromoleculeName: Isoform 2 of Paired amphipathic helix protein Sin3b / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.547133 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAHAGGGSGG SGAGGPAGRG LSGARWGRSG SAGHEKLPVH VEDALTYLDQ VKIRFGSDPA TYNGFLEIMK EFKSQSIDTP GVIRRVSQL FHEHPDLIVG FNAFLPLGYR IDIPKNGKLN IQSPLTSQEN SHNHGDGAED FKQQVPYKED KPQVPLESDS V EFNNAISY ...String:
MAHAGGGSGG SGAGGPAGRG LSGARWGRSG SAGHEKLPVH VEDALTYLDQ VKIRFGSDPA TYNGFLEIMK EFKSQSIDTP GVIRRVSQL FHEHPDLIVG FNAFLPLGYR IDIPKNGKLN IQSPLTSQEN SHNHGDGAED FKQQVPYKED KPQVPLESDS V EFNNAISY VNKIKTRFLD HPEIYRSFLE ILHTYQKEQL NTRGRPFRGM SEEEVFTEVA NLFRGQEDLL SEFGQFLPEA KR SLFTGNG PCEMHSVQKN EHDKTPEHSR KRSRPSLLRP VSAPAKKKMK LRGTKDLSIA AVGKYGTLQE FSFFDKVRRV LKS QEVYEN FLRCIALFNQ ELVSGSELLQ LVSPFLGKFP ELFAQFKSFL GVKELSFAPP MSDRSGDGIS REIDYASCKR IGSS YRALP KTYQQPKCSG RTAICKEVLN DTWVSFPSWS EDSTFVSSKK TPYEEQLHRC EDERFELDVV LETNLATIRV LESVQ KKLS RMAPEDQEKF RLDDSLGGTS EVIQRRAIYR IYGDKAPEII ESLKKNPVTA VPVVLKRLKA KEEEWREAQQ GFNKIW REQ YEKAYLKSLD HQAVNFKQND TKALRSKSLL NEIESVYDEH QEQHSEGRSA PSSEPHLIFV YEDRQILEDA AALISYY VK RQPAIQKEDQ GTIHQLLHQF VPSLFFSQQL DLGASEESAD EDRDSPQGQT TDPSERKKPA PGPHSSPPEE KGAFGDAP A TEQPPLPPPA PHKPLDDVYS LFFANNNWYF FLRLHQTLCS RLLKIYRQAQ KQLLEYRTEK EREKLLCEGR REKGSDPAM ELRLKQPSEV ELEEYYPAFL DMVRSLLEGS IDPTQYEDTL REMFTIHAYV GFTMDKLVQN IARQLHHLVS DDVCLKVVEL YLNEKKRGA AGGNLSSRCV RAARETSYQW KAERCMADEN CFKVMFLQRK GQVIMTIELL DTEEAQTEDP VEVQHLARYV E QYVGTEGA SSSPTEGFLL KPVFLQRNLK KFRRRWQSEQ ARALRGEARS SWKRLVGVES ACDVDCRFKL STHKMVFIVN SE DYMYRRG TLCRAKQVQP LVLLRHHQHF EEWHSRWLED NVTVEAASLV QDWLMGEEDE DMVPCKTLCE TVHVHGLPVT RYR VQYSRR PASP

UniProtKB: Paired amphipathic helix protein Sin3b

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Macromolecule #2: Histone deacetylase 2

MacromoleculeName: Histone deacetylase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.443156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAYSQGGGKK KVCYYYDGDI GNYYYGQGHP MKPHRIRMTH NLLLNYGLYR KMEIYRPHKA TAEEMTKYHS DEYIKFLRSI RPDNMSEYS KQMQRFNVGE DCPVFDGLFE FCQLSTGGSV AGAVKLNRQQ TDMAVNWAGG LHHAKKSEAS GFCYVNDIVL A ILELLKYH ...String:
MAYSQGGGKK KVCYYYDGDI GNYYYGQGHP MKPHRIRMTH NLLLNYGLYR KMEIYRPHKA TAEEMTKYHS DEYIKFLRSI RPDNMSEYS KQMQRFNVGE DCPVFDGLFE FCQLSTGGSV AGAVKLNRQQ TDMAVNWAGG LHHAKKSEAS GFCYVNDIVL A ILELLKYH QRVLYIDIDI HHGDGVEEAF YTTDRVMTVS FHKYGEYFPG TGDLRDIGAG KGKYYAVNFP MRDGIDDESY GQ IFKPIIS KVMEMYQPSA VVLQCGADSL SGDRLGCFNL TVKGHAKCVE VVKTFNLPLL MLGGGGYTIR NVARCWTYET AVA LDCEIP NELPYNDYFE YFGPDFKLHI SPSNMTNQNT PEYMEKIKQR LFENLRMLPH APGVQMQAIP EDAVHEDSGD EDGE DPDKR ISIRASDKRI ACDEEFSDSE DEGEGGRRNV ADHKKGAKKA RIEEDKKETE DKKTDVKEED KSKDNSGEKT DTKGT KSEQ LSNP

UniProtKB: Histone deacetylase 2

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Macromolecule #3: PHD finger protein 12

MacromoleculeName: PHD finger protein 12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.841586 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWEKMETKTI VYDLDTSGGL MEQIQALLAP PKTDEAEKRS RKPEKEPRRS GRATNHDSCD SCKEGGDLLC CDHCPAAFHL QCCNPPLSE EMLPPGEWMC HRCTVRRKKR EQKKELGHVN GLVDKSGKRT TSPSSDTDLL DRSASKTELK AIAHARILER R ASRPGTPT ...String:
MWEKMETKTI VYDLDTSGGL MEQIQALLAP PKTDEAEKRS RKPEKEPRRS GRATNHDSCD SCKEGGDLLC CDHCPAAFHL QCCNPPLSE EMLPPGEWMC HRCTVRRKKR EQKKELGHVN GLVDKSGKRT TSPSSDTDLL DRSASKTELK AIAHARILER R ASRPGTPT SSASTETPTS EQNDVDEDII DVDEEPVAAE PDYVQPQLRR PFELLIAAAM ERNPTQFQLP NELTCTTALP GS SKRRRKE ETTGKNVKKT QHELDHNGLV PLPVKVCFTC NRSCRVAPLI QCDYCPLLFH MDCLEPPLTA MPLGRWMCPN HIE HVVLNQ KNMTLSNRCQ VFDRFQDTVS QHVVKVDFLN RIHKKHPPNR RVLQSVKRRS LKVPDAIKSQ YQFPPPLIAP AAIR DGELI CNGIPEESQM HLLNSEHLAT QAEQQEWLCS VVALQCSILK HLSAKQMPSH WDSEQTEKAD IKPVIVTDSS VTTSL QTAD KTPTPSHYPL SCPSGISTQN SLSCSPPHQS PALEDIGCSS CAEKSKKTPC GTANGPVNTE VKANGPHLYS SPTDST DPR RLPGANTPLP GLSHRQGWPR PLTPPAAGGL QNHTVGIIVK TENATGPSSC PQRSLVPVPS LPPSIPSSCA SIENTST LQ RKTVQSQIGP PLTDSRPLGS PPNATRVLTP PQAAGDGILA TTANQRFSSP APSSDGKVSP GTLSIGSALT VPSFPANS T AMVDLTNSLR AFMDVNGEIE INMLDEKLIK FLALQRIHQL FPSRVQPSPG SVGTHQLASG GHHIEVQRKE VQARAVFYP LLGLGGAVNM CYRTLYIGTG ADMDVCLTNY GHCNYVSGKH ACIFYDENTK HYELLNYSEH GTTVDNVLYS CDFSEKTPPT PPSSIVAKV QSVIRRRRHQ KQDEEPSEEA AMMSSQAQGP QRRPCNCKAS SSSLIGGSGA GWEGTALLHH GSYIKLGCLQ F VFSITEFA TKQPKGDASL LQDGVLAEKL SLKPHQGPVL RSNSVP

UniProtKB: PHD finger protein 12

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Macromolecule #4: Mortality factor 4-like protein 1

MacromoleculeName: Mortality factor 4-like protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.540484 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPKQDPKPK FQEGERVLCF HGPLLYEAKC VKVAIKDKQV KYFIHYSGWN KKSAVRPRRS EKSLKTHEDI VALFPVPEGA PSVHHPLLT SSWDEWVPES RVLKYVDTNL QKQRELQKAN QEQYAEGKMR GAAPGKKTSG LQQKNVEVKT KKNKQKTPGN G DGGSTSET ...String:
MAPKQDPKPK FQEGERVLCF HGPLLYEAKC VKVAIKDKQV KYFIHYSGWN KKSAVRPRRS EKSLKTHEDI VALFPVPEGA PSVHHPLLT SSWDEWVPES RVLKYVDTNL QKQRELQKAN QEQYAEGKMR GAAPGKKTSG LQQKNVEVKT KKNKQKTPGN G DGGSTSET PQPPRKKRAR VDPTVENEET FMNRVEVKVK IPEELKPWLV DDWDLITRQK QLFYLPAKKN VDSILEDYAN YK KSRGNTD NKEYAVNEVV AGIKEYFNVM LGTQLLYKFE RPQYAEILAD HPDAPMSQVY GAPHLLRLFV RIGAMLAYTP LDE KSLALL LNYLHDFLKY LAKNSATLFS ASDYEVAPPE YHRKAV

UniProtKB: Mortality factor 4-like protein 1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49835
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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