8HXX: Histone deacetylase complex Rpd3S
Cryo-EM structure of the histone deacetylase complex Rpd3S. Determined by electron microscopy at 3.0 Å resolution. Released 27 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Saccharomyces cerevisiae, Xenopus laevis
- Chains
- 7
- Atoms
- 14,873
- Mol. weight
- 488.23 kDa
- Ligands
- ZN
- Released
- 27 Sept 2023
Explore 8HXX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8HXX contains 95 α-helices and 47 β-strands across 7 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 E: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 11 |
| α-helix | 19-21 | 3 | |
Chain K: 26 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 663-676 | 14 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-709 | 11 | |
| α-helix | 714-724 | 11 | |
| β-strand | 756-757 | 2 | 1 |
| α-helix | 760-763 | 4 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782-783 | 2 | 1 |
| α-helix | 786-789 | 4 | |
| α-helix | 797-799 | 3 | |
| α-helix | 802-839 | 38 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 887-928 | 42 | |
| α-helix | 935-942 | 8 | |
| α-helix | 945-963 | 19 | |
| β-strand | 975-978 | 4 | 2 |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1026-1031 | 6 | |
| β-strand | 1129-1130 | 2 | 3 |
| β-strand | 1135-1140 | 6 | 2 |
| α-helix | 1142-1163 | 22 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1179-1183 | 5 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1232 | 12 | |
| α-helix | 1237-1239 | 3 | |
| α-helix | 1242-1257 | 16 | |
| α-helix | 1263-1274 | 12 | |
| β-strand | 1278-1279 | 2 | 3 |
| α-helix | 1280-1293 | 14 | |
| β-strand | 1301-1306 | 6 | 2 |
| β-strand | 1311-1316 | 6 | 2 |
Chain L: 21 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 21-24 | 4 | 4 |
| α-helix | 27-31 | 5 | |
| α-helix | 43-54 | 12 | |
| α-helix | 57-60 | 4 | |
| β-strand | 62-66 | 5 | 4 |
| α-helix | 67-69 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 92-94 | 3 | |
| α-helix | 99-103 | 5 | |
| β-strand | 106-107 | 2 | 5 |
| β-strand | 110 | 1 | 5 |
| α-helix | 116-135 | 20 | |
| β-strand | 141-144 | 4 | 4 |
| β-strand | 158 | 1 | 6 |
| β-strand | 161 | 1 | 6 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 4 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-210 | 8 | 4 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 4 |
| α-helix | 244-262 | 19 | |
| β-strand | 266-271 | 6 | 4 |
| α-helix | 273-275 | 3 | |
| β-strand | 276 | 1 | 7 |
| β-strand | 286 | 1 | 7 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-309 | 5 | 4 |
| α-helix | 315-328 | 14 | |
| α-helix | 344-347 | 4 | |
| α-helix | 356-358 | 3 | |
| α-helix | 366-379 | 14 | |
| α-helix | 380-382 | 3 | |
Chain M: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-236 | 11 | |
| α-helix | 237-241 | 5 | |
| β-strand | 244-246 | 3 | 8 |
| β-strand | 253 | 1 | 9 |
| α-helix | 254-268 | 15 | |
| α-helix | 272-296 | 25 | |
| α-helix | 303-315 | 13 | |
| α-helix | 322-325 | 4 | |
| β-strand | 327 | 1 | 9 |
| α-helix | 328-343 | 16 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-373 | 4 | |
| β-strand | 387-389 | 3 | 8 |
| α-helix | 390-391 | 2 | |
| α-helix | 392-398 | 7 | |
Chain N: 19 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 85-87 | 3 | 10 |
| β-strand | 93-96 | 4 | 10 |
| α-helix | 101-103 | 3 | |
| α-helix | 121-127 | 7 | |
| α-helix | 172-175 | 4 | |
| β-strand | 177-179 | 3 | 4 |
| α-helix | 258-260 | 3 | |
| β-strand | 271-274 | 4 | 11 |
| α-helix | 275 | 1 | |
| β-strand | 281-283 | 3 | 11 |
| α-helix | 290-292 | 3 | |
| α-helix | 304-314 | 11 | |
| α-helix | 319-329 | 11 | |
| α-helix | 337-342 | 6 | |
| α-helix | 347-348 | 2 | |
| α-helix | 355-358 | 4 | |
| β-strand | 365-366 | 2 | 12 |
| β-strand | 372-373 | 2 | 12 |
| α-helix | 378-382 | 5 | |
| α-helix | 383-387 | 5 | |
| β-strand | 407 | 1 | 13 |
| β-strand | 414 | 1 | 13 |
| α-helix | 431-433 | 3 | |
| α-helix | 434-436 | 3 | |
| β-strand | 437-439 | 3 | 14 |
| β-strand | 446-448 | 3 | 14 |
| α-helix | 463-464 | 2 | |
| α-helix | 470-471 | 2 | |
| β-strand | 473-477 | 5 | 15 |
| β-strand | 489-493 | 5 | 15 |
| α-helix | 494-497 | 4 | |
| β-strand | 505-506 | 2 | 16 |
| β-strand | 520-522 | 3 | 16 |
| α-helix | 546-576 | 31 | |
Chain O: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-240 | 15 | |
| β-strand | 253 | 1 | 17 |
| α-helix | 254-268 | 15 | |
| α-helix | 272-292 | 21 | |
| α-helix | 303-313 | 11 | |
| β-strand | 327 | 1 | 17 |
| α-helix | 329-342 | 14 | |
| α-helix | 350-368 | 19 | |
| α-helix | 370-373 | 4 | |
Chain P: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 274 | 1 | 18 |
| β-strand | 281 | 1 | 18 |
| α-helix | 291-292 | 2 | |
| α-helix | 296-297 | 2 | |
| α-helix | 304-312 | 9 | |
| α-helix | 316-329 | 14 | |
| α-helix | 331-336 | 6 | |
| α-helix | 337-344 | 8 | |
| α-helix | 355-358 | 4 | |
| α-helix | 534-537 | 4 | |
| α-helix | 538 | 1 | |
| β-strand | 539-542 | 4 | 16 |
| α-helix | 544-579 | 36 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transcriptional regulatory protein SIN3 | K | protein | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Histone deacetylase RPD3 | L | protein | 433 | Saccharomyces cerevisiae | P32561 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | M, O | protein | 401 | Saccharomyces cerevisiae | Q12432 (AlphaFold model) |
| RCO1 isoform 1 | N, P | protein | 684 | Saccharomyces cerevisiae | Q04779 (AlphaFold model) |
| Histone H3 | E | protein | 135 | Xenopus laevis | P84233 |
Sequence of entity 1 (K), FASTA
>8HXX_1 Transcriptional regulatory protein SIN3 (chains K)
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 2 (L), FASTA
>8HXX_2 Histone deacetylase RPD3 (chains L)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 3 (M, O), FASTA
>8HXX_3 Chromatin modification-related protein EAF3 (chains M, O)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 4 (N, P), FASTA
>8HXX_4 RCO1 isoform 1 (chains N, P)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Sequence of entity 5 (E), FASTA
>8HXX_5 Histone H3 (chains E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 7 |
Primary citation
Structure of histone deacetylase complex Rpd3S bound to nucleosome. Li, W., Cui, H., Lu, Z. et al. Nat Struct Mol Biol (2023) 30:1893-1901. DOI 10.1038/s41594-023-01121-5 · PubMed
Other PDB entries of the same protein (UniProt P22579 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6XAW 1.84 Å, Crystal Structure Analysis of SIN3-UME6
- 6XDJ 2.2 Å, Crystal Structure Analysis of MBP-SIN3
- 8HPO 2.6 Å, Cryo-EM structure of a SIN3/HDAC complex from budding yeast
- 8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
- 8KD3 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
- 8KD5 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
- 8KD4 2.93 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
- 9V2V 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
- 8KD2 3.02 Å, Rpd3S in complex with 187bp nucleosome
- 8KD6 3.07 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
- 8KD7 3.09 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
- 8HXY 3.1 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome
Browse structure collections
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