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- EMDB-16449: Cryo-EM structure of the human SIN3B full-length complex at 3.4 A... -

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Basic information

Entry
Database: EMDB / ID: EMD-16449
TitleCryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution
Map dataSIN3B full-length complex
Sample
  • Complex: Human SIN3B 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 IONCalcium
Function / homology
Function and homology information


autosome / protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol ...autosome / protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / negative regulation of MHC class II biosynthetic process / NuRD complex / positive regulation of interleukin-1 production / regulation of cell fate specification / XY body / negative regulation of stem cell population maintenance / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of transcription by competitive promoter binding / regulation of double-strand break repair / ESC/E(Z) complex / regulation of stem cell differentiation / STAT3 nuclear events downstream of ALK signaling / cellular response to dopamine / histone deacetylase / cardiac muscle hypertrophy / protein lysine deacetylase activity / positive regulation of signaling receptor activity / response to caffeine / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / NuA4 histone acetyltransferase complex / embryonic digit morphogenesis / positive regulation of oligodendrocyte differentiation / positive regulation of stem cell population maintenance / Sin3-type complex / positive regulation of double-strand break repair via homologous recombination / Notch-HLH transcription pathway / Y chromosome / dendrite development / eyelid development in camera-type eye / X chromosome / odontogenesis of dentin-containing tooth / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / response to amyloid-beta / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / NF-kappaB binding / positive regulation of collagen biosynthetic process / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin formation / MECP2 regulates neuronal receptors and channels / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of TP53 Activity through Acetylation / cellular response to transforming growth factor beta stimulus / response to amphetamine / heat shock protein binding / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / SUMOylation of chromatin organization proteins / phosphatidylinositol binding / negative regulation of cell migration / transcription corepressor binding / response to cocaine / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to nicotine / Regulation of PTEN gene transcription / promoter-specific chromatin binding / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / double-strand break repair via homologous recombination / circadian regulation of gene expression / protein modification process / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / Cytoprotection by HMOX1 / 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 / transcription corepressor activity / nucleosome / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / cellular response to heat / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / fibroblast proliferation / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / 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 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 ...PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / 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: 3.4 Å
AuthorsAlfieri C / Wan SM / Muhammad R
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
DepositionJan 10, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16449.png

Downloads & links

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Map

FileDownload / File: emd_16449.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSIN3B full-length complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 200 pix.
= 226.8 Å		1.13 Å/pix.
x 200 pix.
= 226.8 Å		1.13 Å/pix.
x 200 pix.
= 226.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.134 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.012397126 - 1.8502533
Average (Standard dev.)0.0019929844 (±0.03185888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 226.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SIN3B full-length complex half map 1

Fileemd_16449_half_map_1.map
AnnotationSIN3B full-length complex half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SIN3B full-length complex half map 2

Fileemd_16449_half_map_2.map
AnnotationSIN3B full-length complex half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SIN3B complex

EntireName: Human SIN3B complex
Components
  • Complex: Human SIN3B 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 IONCalcium

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Supramolecule #1: Human SIN3B complex

SupramoleculeName: Human SIN3B complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 385 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

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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

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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

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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 (butterflies/moths)
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

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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

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38352

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