8HPO: SIN3/HDAC complex from budding yeast

Cryo-EM structure of a SIN3/HDAC complex from budding yeast. Determined by electron microscopy at 2.6 Å resolution. Released 3 May 2023.

Method
Electron microscopy
Resolution
2.6 Å
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains
11
Atoms
27,950
Mol. weight
727.58 kDa
Ligands
ZN
Released
3 May 2023

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

Secondary structure: helices and β-sheets

8HPO contains 166 α-helices and 107 β-strands across 11 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: 36 helices, 7 β-strands

ElementResiduesLengthSheet
α-helix643-6486
α-helix663-67614
α-helix679-69315
α-helix699-71012
α-helix714-72411
β-strand750-751221
β-strand755-757321
α-helix758-7592
α-helix761-7633
α-helix773-7764
β-strand782-784321
α-helix796-7983
α-helix803-83836
α-helix844-8474
α-helix862-8709
α-helix876-88510
α-helix887-8904
α-helix895-92329
α-helix925-9273
α-helix932-94110
α-helix945-9506
α-helix968-9714
β-strand975-977322
α-helix983-99614
α-helix1004-102219
α-helix1026-103813
α-helix1065-10684
β-strand1135-1140622
α-helix1142-117231
α-helix1179-11835
α-helix1190-11934
α-helix1203-121614
α-helix1221-123111
α-helix1237-12393
α-helix1242-125312
α-helix1260-127314
α-helix1281-129313
β-strand1300-1306722
β-strand1311-1317722
α-helix1325-13273
α-helix1330-134213
α-helix1346-13472
α-helix1362-137110
Chain B: 33 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix654-6563
α-helix657-6593
α-helix668-6769
α-helix679-69315
α-helix699-71012
α-helix714-72310
β-strand734-735226
α-helix7371
β-strand738127
α-helix7391
β-strand750128
β-strand755-757328
α-helix758-7592
α-helix765-7673
α-helix772-7776
β-strand782-784328
α-helix796-7983
α-helix802-83938
α-helix861-87111
α-helix877-8826
α-helix893-92533
α-helix931-9388
α-helix945-96420
β-strand975-977329
α-helix983-99614
α-helix1004-102118
α-helix1026-103914
α-helix1065-10695
β-strand1130130
β-strand1135-1140629
α-helix1142-116322
α-helix1165-117410
α-helix1190-11945
α-helix1203-121614
α-helix1221-123111
α-helix1234-12396
α-helix1242-12465
α-helix1249-12568
α-helix1260-127314
β-strand1278130
α-helix1280-129112
β-strand1300-1306729
β-strand1311-1317729
α-helix1331-134212
Chain C: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-3628
α-helix43-5412
α-helix65-7915
α-helix82-11332
α-helix132-14615
Chain D: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix15-3420
α-helix41-5414
α-helix62-14079
α-helix293-2964
α-helix301-31515
α-helix317-3204
Chain E: 12 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix23-3614
α-helix53-564
α-helix71-744
α-helix84-863
β-strand90-93425
β-strand96-99425
β-strand100124
α-helix162-1654
α-helix174-1774
α-helix181-1833
α-helix190-21728
α-helix225-2262
α-helix233-2353
α-helix298-3014
α-helix319-37355
Chain F: 18 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand21-24410
α-helix29-313
α-helix43-5412
α-helix57-604
β-strand62-64310
α-helix65-706
α-helix71-744
α-helix80-889
α-helix94-974
α-helix98-1036
α-helix116-13520
β-strand141-144410
β-strand153111
β-strand156111
β-strand158112
β-strand161112
α-helix165-17410
β-strand180-184510
α-helix191-1966
β-strand203-210810
α-helix227-2293
β-strand233-238610
α-helix244-26118
β-strand267-270410
α-helix288-29912
β-strand305-308410
α-helix315-32915
β-strand337113
α-helix338-3403
β-strand352113
α-helix366-37914
Chain G: 20 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix201
β-strand21-24414
α-helix29-313
α-helix43-5412
α-helix57-593
β-strand61-64414
α-helix66-705
α-helix71-744
α-helix80-889
α-helix95-973
α-helix100-1034
β-strand106115
β-strand110115
α-helix116-13520
β-strand141-144414
β-strand153116
β-strand156116
β-strand158117
β-strand161117
α-helix165-17612
β-strand180-184514
α-helix191-1966
β-strand203-210814
α-helix227-2293
β-strand233-238614
α-helix244-26118
β-strand266-270514
β-strand276118
β-strand286118
α-helix288-29912
β-strand305-308414
α-helix315-32915
β-strand337119
α-helix345-3473
β-strand352119
α-helix356-3583
α-helix360-3623
α-helix366-37914
Chain H: 6 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix172-21544
α-helix231-29464
β-strand309123
α-helix337-3415
β-strand353123
α-helix356-37924
β-strand383124
α-helix386-3894
α-helix394-4029

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Transcriptional regulatory protein UME1Kprotein460Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q03010 (AlphaFold model)
Transcriptional regulatory protein SDS3Dprotein327Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P40505 (AlphaFold model)
Histone deacetylase RPD3Fprotein433Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32561 (AlphaFold model)
Histone deacetylase RPD3Gprotein433Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32561 (AlphaFold model)
Transcriptional regulatory protein SAP30Iprotein201Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P38429 (AlphaFold model)
Transcriptional regulatory protein SIN3A, Bprotein1536Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P22579
Transcriptional regulatory protein DEP1Hprotein405Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P31385
Transcriptional regulatory protein PHO23Cprotein330Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P50947
Transcriptional regulatory protein RXT2Eprotein430Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P38255
Transcriptional regulatory protein RXT3Jprotein294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q07458
Sequence of entity 1 (K), FASTA
>8HPO_1 Transcriptional regulatory protein UME1 (chains K)
MSTLDIAEDNKIKNEEFKIWKKSIPSLYQHISSLKPIFGSGVDESPSTLRSIVFTNDSSC
NKSKGVLSVPLLYSQGSEIFEVDCIVPLGLHYKKPESISEPLVQPDYTMESQKVEQTVLI
PKWEFKGETIAKMIYVDNSEINVKVIALSTNGSLAWFREGVKSPVYTMMEPSTSLSSASS
GNQNKPCVDFAISNDSKTLTVTKEKHLDNENATIKLIDNSGKIGEVLRTIPVPGIKNIQE
IKFLNNQIFATCSDDGIIRFWGNEIGKKPLWILNDSLDGKTTCFAASPFVDTLFMTGTSG
GALKVWDIRAVIALGDADAELNINQGHNKVNELFKVHHFYSEQVSKIEFSSISPMEVVTI
GGLGNVYHWNFEPVFAIYNEIHEDFQGIISDELEAESMAFYHTEGCRREIGENNKVNTVA
YHKYIEDLVATVDSDGLLTVYKPFTGKVLDGSREVGAAKS
Sequence of entity 2 (D), FASTA
>8HPO_2 Transcriptional regulatory protein SDS3 (chains D)
MAIQKVSNKDLSRKDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNG
QYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSS
IEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESA
TDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTY
KSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLK
PDEVTEDISLIRELTGQPPAPFRLRSD
Sequence of entity 3 (F), FASTA
>8HPO_3 Histone deacetylase RPD3 (chains F)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 4 (G), FASTA
>8HPO_4 Histone deacetylase RPD3 (chains G)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 5 (I), FASTA
>8HPO_5 Transcriptional regulatory protein SAP30 (chains I)
MARPVNTNAETESRGRPTQGGGYASNNNGSCNNNNGSNNNNNNNNNNNNNSNNSNNNNGP
TSSGRTNGKQRLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQ
LDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDC
IPQFIYKVKNQKKKFKMEFRG
Sequence of entity 6 (A, B), FASTA
>8HPO_6 Transcriptional regulatory protein SIN3 (chains A, B)
MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKE
EDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINA
SLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQRPQDCKEV
PAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPD
IYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPI
RVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQD
QQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKT
RFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQ
QVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQN
LPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLR
TSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNI
SLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWF
KNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLND
EWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIEN
MTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQ
KDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQT
NKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISL
FFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRS
NDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFA
NTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVG
EDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDA
KTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALD
DLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDGTEVDEEFS
PEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISK
FLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLD
SSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ
Sequence of entity 7 (H), FASTA
>8HPO_7 Transcriptional regulatory protein DEP1 (chains H)
MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEK
SLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKS
QELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRM
TALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHR
AYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVI
PDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIV
DRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQ
Sequence of entity 8 (C), FASTA
>8HPO_8 Transcriptional regulatory protein PHO23 (chains C)
MSSPANLFPGLNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNK
DHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNTEIPRG
LRLGVDNHPAMHLHHELMEKIESKSNSKSSQALKSESRREAMAANRRQGEHYSASTHQQD
DSKNDANYGGSRHESQDHTGNNTNSRKRANAANTNNADPETKKRKRRVATTAVSPSTIST
ATAVNNGRIGTSTASRGVSSVGNSNNSRISRPKTNDYGEPLYCYCNQVAYGEMVGCDGAD
CELEWFHLPCIGLETLPKGKWYCDDCKKKL
Sequence of entity 9 (E), FASTA
>8HPO_9 Transcriptional regulatory protein RXT2 (chains E)
MTIRSSMKNNAELESKSVLANESNIISTFTRRIIKEKSGNYQVLKRSLDGKLIYPEATGI
SSNRGNKLLQRSEVVTRRDLNNSKPMIEQTVFYNGSEHRLLQTNIVTDSRRKRIKFTPDI
NVEPVLVGDENDIDGSEKEDENITDEYYGEEDDDDLSKLVNVKEILTPILSLGDIINHKT
ISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNL
TLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNAL
LSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKAN
RIRGRILNWSREYLGISDDDITIPVALRVVKRGLISATTNKTTNFEEEIENTMEDGVVDD
NEPDEEANRA
Sequence of entity 10 (J), FASTA
>8HPO_10 Transcriptional regulatory protein RXT3 (chains J)
MSVSEQDPNRAYRETQSQIYKLQETLLNSARTKNKQEEGQESNTHSFPEQYMHYQNGRNS
AYDLPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDN
TLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILV
LRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYP
SVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQRLDRDKPHEPNGYIKNLKWT

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2

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

Primary citation

Structure of a SIN3-HDAC complex from budding yeast. Guo, Z., Chu, C., Lu, Y. et al. Nat Struct Mol Biol (2023) 30:753-760. DOI 10.1038/s41594-023-00975-z · PubMed

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