8BPB: Human SIN3B histone deacetylase core complex

Cryo-EM structure of the human SIN3B histone deacetylase core complex at 2.8 Angstrom. Determined by electron microscopy at 2.8 Å resolution. Released 10 May 2023.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Homo sapiens
Chains
3
Atoms
8,384
Mol. weight
226.58 kDa
Ligands
CA, ZN
Released
10 May 2023

Explore 8BPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BPB contains 53 α-helices and 25 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 30 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix305-31814
α-helix322-33312
α-helix334-3385
α-helix341-3488
α-helix356-36611
β-strand396-39721
β-strand401-40331
α-helix404-4052
α-helix410-4123
α-helix418-4236
β-strand428-43031
α-helix447-48337
α-helix488-4914
α-helix507-51610
α-helix517-5193
α-helix520-52910
α-helix531-56030
α-helix564-5729
α-helix576-58611
α-helix589-60921
β-strand620-62452
α-helix627-64216
α-helix649-6579
α-helix658-6625
α-helix663-6664
β-strand739-74572
α-helix747-78539
α-helix789-7913
α-helix806-8083
α-helix809-82820
α-helix833-84412
α-helix845-8517
α-helix854-87017
α-helix872-88716
β-strand892-89322
α-helix897-91418
β-strand921-92882
β-strand931-93882
Chain B: 18 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand13-1533
α-helix20-223
α-helix34-4512
β-strand53-5533
α-helix57-615
α-helix62-654
α-helix71-799
α-helix82-843
α-helix86-883
α-helix89-946
α-helix107-12620
β-strand132-13543
β-strand14914
β-strand15214
α-helix156-1649
β-strand171-17553
α-helix182-1876
β-strand194-20183
α-helix218-2203
β-strand224-22963
α-helix235-25319
β-strand257-26153
β-strand26715
β-strand27715
α-helix279-29113
β-strand296-29943
α-helix306-32015
β-strand32816
α-helix329-3313
α-helix335-3384
β-strand34316
α-helix357-37115
Chain C: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix21-277
β-strand27417
β-strand286-28837
β-strand295-29737
α-helix304-3052
α-helix320-3234
α-helix331-3399
α-helix348-35912

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Isoform 2 of Paired amphipathic helix protein Sin3bAprotein1130Homo sapiensO75182 (AlphaFold model)
Histone deacetylase 2Bprotein488Homo sapiensQ92769 (AlphaFold model)
PHD finger protein 12Cprotein364Homo sapiensQ96QT6 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8BPB_1 Isoform 2 of Paired amphipathic helix protein Sin3b (chains A)
MAHAGGGSGGSGAGGPAGRGLSGARWGRSGSAGHEKLPVHVEDALTYLDQVKIRFGSDPA
TYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNAFLPLGYRIDIPKNGKLNI
QSPLTSQENSHNHGDGAEDFKQQVPYKEDKPQVPLESDSVEFNNAISYVNKIKTRFLDHP
EIYRSFLEILHTYQKEQLNTRGRPFRGMSEEEVFTEVANLFRGQEDLLSEFGQFLPEAKR
SLFTGNGPCEMHSVQKNEHDKTPEHSRKRSRPSLLRPVSAPAKKKMKLRGTKDLSIAAVG
KYGTLQEFSFFDKVRRVLKSQEVYENFLRCIALFNQELVSGSELLQLVSPFLGKFPELFA
QFKSFLGVKELSFAPPMSDRSGDGISREIDYASCKRIGSSYRALPKTYQQPKCSGRTAIC
KEVLNDTWVSFPSWSEDSTFVSSKKTPYEEQLHRCEDERFELDVVLETNLATIRVLESVQ
KKLSRMAPEDQEKFRLDDSLGGTSEVIQRRAIYRIYGDKAPEIIESLKKNPVTAVPVVLK
RLKAKEEEWREAQQGFNKIWREQYEKAYLKSLDHQAVNFKQNDTKALRSKSLLNEIESVY
DEHQEQHSEGRSAPSSEPHLIFVYEDRQILEDAAALISYYVKRQPAIQKEDQGTIHQLLH
QFVPSLFFSQQLDLGASEESADEDRDSPQGQTTDPSERKKPAPGPHSSPPEEKGAFGDAP
ATEQPPLPPPAPHKPLDDVYSLFFANNNWYFFLRLHQTLCSRLLKIYRQAQKQLLEYRTE
KEREKLLCEGRREKGSDPAMELRLKQPSEVELEEYYPAFLDMVRSLLEGSIDPTQYEDTL
REMFTIHAYVGFTMDKLVQNIARQLHHLVSDDVCLKVVELYLNEKKRGAAGGNLSSRCVR
AARETSYQWKAERCMADENCFKVMFLQRKGQVIMTIELLDTEEAQTEDPVEVQHLARYVE
QYVGTEGASSSPTEGFLLKPVFLQRNLKKFRRRWQSEQARALRGEARSSWKRLVGVESAC
DVDCRFKLSTHKMVFIVNSEDYMYRRGTLCRAKQVQPLVLLRHHQHFEEWHSRWLEDNVT
VEAASLVQDWLMGEEDEDMVPCKTLCETVHVHGLPVTRYRVQYSRRPASP
Sequence of entity 2 (B), FASTA
>8BPB_2 Histone deacetylase 2 (chains B)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEE
FSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGT
KSEQLSNP
Sequence of entity 3 (C), FASTA
>8BPB_3 PHD finger protein 12 (chains C)
MWEKMETKTIVYDLDTSGGLMEQIQALLAPPKTDEAEKRSRKPEKEPRRSGRATNHDSCD
SCKEGGDLLCCDHCPAAFHLQCCNPPLSEEMLPPGEWMCHRCTVRRKKREQKKELGHVNG
LVDKSGKRTTSPSSDTDLLDRSASKTELKAIAHARILERRASRPGTPTSSASTETPTSEQ
NDVDEDIIDVDEEPVAAEPDYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGS
SKRRRKEETTGKNVKKTQHELDHNGLVPLPVKVCFTCNRSCRVAPLIQCDYCPLLFHMDC
LEPPLTAMPLGRWMCPNHIEHVVLNQKNMTLSNRCQVFDRFQDTVSQHVVKVDFLNRIHK
KHPP

Ligands and cofactors

IDNameFormulaCopies
CACalcium ionCa2
ZNZinc ionZn3

Water and common crystallization additives (ACT) are not listed.

Primary citation

Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Wan, M.S.M., Muhammad, R., Koliopoulos, M.G. et al. Nat Commun (2023) 14:2556-2556. DOI 10.1038/s41467-023-38276-0 · PubMed

Other PDB entries of the same protein (UniProt O75182 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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