8KC7: Rpd3S histone deacetylase complex
Rpd3S histone deacetylase complex. Determined by electron microscopy at 3.46 Å resolution. Released 13 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.46 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 6
- Atoms
- 14,326
- Mol. weight
- 466.02 kDa
- Released
- 13 Sept 2023
Explore 8KC7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8KC7 contains 83 α-helices and 40 β-strands across 6 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: 20 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 1 |
| α-helix | 29-31 | 3 | |
| α-helix | 44-52 | 9 | |
| α-helix | 57-59 | 3 | |
| β-strand | 62-64 | 3 | 1 |
| β-strand | 65 | 1 | 2 |
| α-helix | 66-69 | 4 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-86 | 7 | |
| α-helix | 94-97 | 4 | |
| α-helix | 98-103 | 6 | |
| α-helix | 116-135 | 20 | |
| β-strand | 141-144 | 4 | 1 |
| β-strand | 158 | 1 | 3 |
| β-strand | 161 | 1 | 3 |
| α-helix | 165-173 | 9 | |
| β-strand | 180-184 | 5 | 1 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-210 | 8 | 1 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 1 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 1 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 1 |
| α-helix | 315-329 | 15 | |
| β-strand | 337 | 1 | 4 |
| α-helix | 338-340 | 3 | |
| α-helix | 344-346 | 3 | |
| β-strand | 352 | 1 | 4 |
| α-helix | 356-358 | 3 | |
| α-helix | 366-380 | 15 | |
| α-helix | 381-383 | 3 | |
| β-strand | 414 | 1 | 2 |
Chain B: 30 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 668-676 | 9 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-709 | 11 | |
| α-helix | 714-724 | 11 | |
| β-strand | 756-757 | 2 | 5 |
| α-helix | 758-759 | 2 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782-783 | 2 | 5 |
| α-helix | 786-789 | 4 | |
| α-helix | 797-799 | 3 | |
| α-helix | 802-839 | 38 | |
| α-helix | 844-847 | 4 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 891-921 | 31 | |
| α-helix | 924-928 | 5 | |
| α-helix | 932-941 | 10 | |
| α-helix | 945-956 | 12 | |
| α-helix | 964-965 | 2 | |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1021 | 18 | |
| β-strand | 1136 | 1 | 6 |
| β-strand | 1139-1140 | 2 | 6 |
| α-helix | 1142-1163 | 22 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1176-1178 | 3 | |
| α-helix | 1179-1183 | 5 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1232 | 12 | |
| α-helix | 1237-1239 | 3 | |
| α-helix | 1242-1255 | 14 | |
| α-helix | 1260-1272 | 13 | |
| α-helix | 1282-1292 | 11 | |
| α-helix | 1299 | 1 | |
| β-strand | 1300-1305 | 6 | 6 |
| β-strand | 1312-1317 | 6 | 6 |
Chain D: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-236 | 11 | |
| α-helix | 237-241 | 5 | |
| β-strand | 244-245 | 2 | 7 |
| α-helix | 254-266 | 13 | |
| α-helix | 274-292 | 19 | |
| α-helix | 300-302 | 3 | |
| α-helix | 303-315 | 13 | |
| α-helix | 328-344 | 17 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-373 | 4 | |
| β-strand | 388-389 | 2 | 7 |
| α-helix | 392-398 | 7 | |
Chain E: 13 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-56 | 4 | |
| β-strand | 263 | 1 | 8 |
| β-strand | 273-274 | 2 | 8 |
| β-strand | 281-282 | 2 | 8 |
| α-helix | 306-309 | 4 | |
| β-strand | 312 | 1 | 9 |
| β-strand | 316 | 1 | 9 |
| α-helix | 322-325 | 4 | |
| α-helix | 326-328 | 3 | |
| α-helix | 334-336 | 3 | |
| α-helix | 337-342 | 6 | |
| α-helix | 358-360 | 3 | |
| β-strand | 365-366 | 2 | 10 |
| β-strand | 372-373 | 2 | 10 |
| β-strand | 376 | 1 | 11 |
| α-helix | 399-401 | 3 | |
| α-helix | 402-406 | 5 | |
| β-strand | 407 | 1 | 12 |
| β-strand | 414 | 1 | 12 |
| α-helix | 431-433 | 3 | |
| β-strand | 437-439 | 3 | 13 |
| β-strand | 446-448 | 3 | 13 |
| α-helix | 449-451 | 3 | |
| β-strand | 462 | 1 | 11 |
| α-helix | 500-502 | 3 | |
| β-strand | 506-507 | 2 | 14 |
| β-strand | 520-522 | 3 | 14 |
| β-strand | 539-542 | 4 | 14 |
| α-helix | 544-576 | 33 | |
Chain F: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 230-242 | 13 | |
| α-helix | 254-265 | 12 | |
| α-helix | 270-271 | 2 | |
| α-helix | 276-290 | 15 | |
| α-helix | 300-312 | 13 | |
| α-helix | 329-342 | 14 | |
| α-helix | 349-367 | 19 | |
Chain G: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 263 | 1 | 15 |
| β-strand | 268 | 1 | 15 |
| α-helix | 304-312 | 9 | |
| α-helix | 322-328 | 7 | |
| α-helix | 543-577 | 35 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone deacetylase RPD3 | A | protein | 433 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32561 (AlphaFold model) |
| Transcriptional regulatory protein SIN3 | B | protein | 1371 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P22579 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | D, F | protein | 401 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12432 (AlphaFold model) |
| Transcriptional regulatory protein RCO1 | E, G | protein | 733 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q04779 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>8KC7_1 Histone deacetylase RPD3 (chains A)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 2 (B), FASTA
>8KC7_2 Transcriptional regulatory protein SIN3 (chains B)
MHHHHHHHHPQLAMWSHPQFEKGGGSGGGSGGGSWSHPQFEKENLYFQSDYRPLNVKDAL
SYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLP
QGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNV
PMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVD
VEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLE
DFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPAS
GYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMV
HQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSI
VPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEK
VDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFM
PCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNL
RTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHE
HPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTT
KQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNP
DKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSL
LDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEAN
SQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLD
LLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKV
TQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEF
DKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIE
FGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDN
TQKGMVSQKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESET
EKGKITKQEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ
Sequence of entity 3 (D, F), FASTA
>8KC7_3 Chromatin modification-related protein EAF3 (chains D, F)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 4 (E, G), FASTA
>8KC7_4 Transcriptional regulatory protein RCO1 (chains E, G)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSEMHHHHHHHHPQLAMWSHPQFEKGGGSGGGSGGGSWS
HPQFEKENLYFQS
Primary citation
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Dong, S., Li, H., Wang, M. et al. Cell Res (2023) 33:790-801. DOI 10.1038/s41422-023-00869-1 · PubMed
Other PDB entries of the same protein (UniProt P32561 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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
- 8HXX 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S
- 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
- 8HY0 3.1 Å, Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with…
Browse structure collections
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