8BPA: Human SIN3B histone deacetylase complex

Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom. Determined by electron microscopy at 3.7 Å resolution. Released 10 May 2023.

Method
Electron microscopy
Resolution
3.7 Å
Organism
Homo sapiens
Chains
4
Atoms
10,393
Mol. weight
336.78 kDa
Ligands
CA, ZN
Released
10 May 2023

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

Secondary structure: helices and β-sheets

8BPA contains 67 α-helices and 29 β-strands across 4 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: 28 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix305-31814
α-helix321-33515
α-helix341-3488
α-helix356-36611
β-strand396-39721
β-strand401-40331
α-helix404-4052
α-helix410-4123
α-helix418-4236
β-strand428-42921
α-helix447-48337
α-helix488-4936
α-helix507-51610
α-helix520-52910
α-helix531-56030
α-helix568-5725
α-helix576-58611
α-helix589-60921
β-strand620-62452
α-helix628-64114
α-helix649-6579
α-helix658-6625
α-helix663-6664
β-strand739-74572
α-helix747-78539
α-helix789-7913
α-helix805-8084
α-helix809-82820
α-helix833-84412
α-helix845-8506
α-helix854-87017
α-helix872-88716
β-strand892-89322
α-helix897-91519
β-strand921-92882
β-strand931-93882
Chain B: 19 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand13-1533
α-helix35-4511
β-strand53-5533
α-helix56-616
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-helix235-25218
β-strand257-26153
α-helix264-2663
β-strand26715
β-strand27715
α-helix279-29012
β-strand296-29943
α-helix306-32015
β-strand32816
α-helix329-3313
α-helix335-3384
β-strand34316
α-helix347-3493
α-helix357-37216
Chain C: 8 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix21-277
β-strand68-7037
β-strand77-7937
α-helix100-11112
α-helix207-21913
α-helix229-2324
β-strand27418
β-strand287-28828
β-strand295-29628
α-helix304-3052
α-helix321-3244
α-helix331-34111
α-helix348-35912
Chain D: 12 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix205-2117
α-helix212-2165
β-strand21919
α-helix220-2223
α-helix229-24113
α-helix250-26617
α-helix275-2773
α-helix278-28710
α-helix300-31213
α-helix313-3153
α-helix320-33920
α-helix341-3444
β-strand35219
α-helix355-3617

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Isoform 2 of Paired amphipathic helix protein Sin3bAprotein1130Homo sapiensO75182 (AlphaFold model)
Histone deacetylase 2Bprotein488Homo sapiensQ92769 (AlphaFold model)
PHD finger protein 12Cprotein1004Homo sapiensQ96QT6 (AlphaFold model)
Mortality factor 4-like protein 1Dprotein362Homo sapiensQ9UBU8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8BPA_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
>8BPA_2 Histone deacetylase 2 (chains B)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEE
FSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGT
KSEQLSNP
Sequence of entity 3 (C), FASTA
>8BPA_3 PHD finger protein 12 (chains C)
MWEKMETKTIVYDLDTSGGLMEQIQALLAPPKTDEAEKRSRKPEKEPRRSGRATNHDSCD
SCKEGGDLLCCDHCPAAFHLQCCNPPLSEEMLPPGEWMCHRCTVRRKKREQKKELGHVNG
LVDKSGKRTTSPSSDTDLLDRSASKTELKAIAHARILERRASRPGTPTSSASTETPTSEQ
NDVDEDIIDVDEEPVAAEPDYVQPQLRRPFELLIAAAMERNPTQFQLPNELTCTTALPGS
SKRRRKEETTGKNVKKTQHELDHNGLVPLPVKVCFTCNRSCRVAPLIQCDYCPLLFHMDC
LEPPLTAMPLGRWMCPNHIEHVVLNQKNMTLSNRCQVFDRFQDTVSQHVVKVDFLNRIHK
KHPPNRRVLQSVKRRSLKVPDAIKSQYQFPPPLIAPAAIRDGELICNGIPEESQMHLLNS
EHLATQAEQQEWLCSVVALQCSILKHLSAKQMPSHWDSEQTEKADIKPVIVTDSSVTTSL
QTADKTPTPSHYPLSCPSGISTQNSLSCSPPHQSPALEDIGCSSCAEKSKKTPCGTANGP
VNTEVKANGPHLYSSPTDSTDPRRLPGANTPLPGLSHRQGWPRPLTPPAAGGLQNHTVGI
IVKTENATGPSSCPQRSLVPVPSLPPSIPSSCASIENTSTLQRKTVQSQIGPPLTDSRPL
GSPPNATRVLTPPQAAGDGILATTANQRFSSPAPSSDGKVSPGTLSIGSALTVPSFPANS
TAMVDLTNSLRAFMDVNGEIEINMLDEKLIKFLALQRIHQLFPSRVQPSPGSVGTHQLAS
GGHHIEVQRKEVQARAVFYPLLGLGGAVNMCYRTLYIGTGADMDVCLTNYGHCNYVSGKH
ACIFYDENTKHYELLNYSEHGTTVDNVLYSCDFSEKTPPTPPSSIVAKVQSVIRRRRHQK
QDEEPSEEAAMMSSQAQGPQRRPCNCKASSSSLIGGSGAGWEGTALLHHGSYIKLGCLQF
VFSITEFATKQPKGDASLLQDGVLAEKLSLKPHQGPVLRSNSVP
Sequence of entity 4 (D), FASTA
>8BPA_4 Mortality factor 4-like protein 1 (chains D)
MAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKKSAVRPRRS
EKSLKTHEDIVALFPVPEGAPSVHHPLLTSSWDEWVPESRVLKYVDTNLQKQRELQKANQ
EQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARVD
PTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYK
KSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAP
HLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRK
AV

Ligands and cofactors

IDNameFormulaCopies
CACalcium ionCa2
ZNZinc ionZn5

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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