8W9C: Rpd3S complex from budding yeast
Cryo-EM structure of the Rpd3S complex from budding yeast. Determined by electron microscopy at 3.3 Å resolution. Released 15 May 2024.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 15,278
- Mol. weight
- 472.98 kDa
- Ligands
- ZN
- Released
- 15 May 2024
Explore 8W9C in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8W9C contains 87 α-helices and 46 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: 30 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 666-676 | 11 | |
| α-helix | 680-693 | 14 | |
| α-helix | 699-707 | 9 | |
| α-helix | 715-723 | 9 | |
| β-strand | 756-757 | 2 | 1 |
| α-helix | 773-776 | 4 | |
| β-strand | 782-783 | 2 | 1 |
| α-helix | 802-838 | 37 | |
| α-helix | 843-848 | 6 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 887-922 | 36 | |
| α-helix | 925-927 | 3 | |
| α-helix | 932-934 | 3 | |
| α-helix | 945-963 | 19 | |
| α-helix | 969-971 | 3 | |
| β-strand | 975-978 | 4 | 2 |
| α-helix | 984-998 | 15 | |
| α-helix | 1004-1020 | 17 | |
| α-helix | 1026-1037 | 12 | |
| α-helix | 1066-1069 | 4 | |
| α-helix | 1071-1080 | 10 | |
| α-helix | 1119-1126 | 8 | |
| β-strand | 1130 | 1 | 3 |
| β-strand | 1135-1140 | 6 | 2 |
| α-helix | 1142-1173 | 32 | |
| α-helix | 1179-1183 | 5 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1231 | 11 | |
| α-helix | 1237-1241 | 5 | |
| α-helix | 1244-1258 | 15 | |
| α-helix | 1261-1274 | 14 | |
| β-strand | 1278 | 1 | 3 |
| α-helix | 1280-1291 | 12 | |
| β-strand | 1301-1306 | 6 | 2 |
| β-strand | 1311-1316 | 6 | 2 |
| α-helix | 1330-1340 | 11 | |
Chain B: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 21-24 | 4 | 5 |
| α-helix | 29-31 | 3 | |
| α-helix | 43-54 | 12 | |
| α-helix | 57-59 | 3 | |
| β-strand | 62-66 | 5 | 5 |
| α-helix | 67-70 | 4 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| α-helix | 100-103 | 4 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 5 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 5 |
| α-helix | 191-195 | 5 | |
| β-strand | 203-210 | 8 | 5 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 5 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 5 |
| β-strand | 276 | 1 | 11 |
| β-strand | 286 | 1 | 11 |
| α-helix | 288-301 | 14 | |
| β-strand | 307-308 | 2 | 5 |
| α-helix | 315-329 | 15 | |
| β-strand | 337 | 1 | 12 |
| α-helix | 344-346 | 3 | |
| β-strand | 352 | 1 | 12 |
| α-helix | 366-380 | 15 | |
Chain C: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-239 | 14 | |
| β-strand | 244-246 | 3 | 13 |
| β-strand | 253 | 1 | 14 |
| α-helix | 254-265 | 12 | |
| α-helix | 272-296 | 25 | |
| α-helix | 303-316 | 14 | |
| α-helix | 322-324 | 3 | |
| β-strand | 327 | 1 | 14 |
| α-helix | 328-344 | 17 | |
| α-helix | 349-373 | 25 | |
| β-strand | 387-389 | 3 | 13 |
| α-helix | 392-398 | 7 | |
Chain D: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-240 | 15 | |
| β-strand | 244-246 | 3 | 15 |
| α-helix | 254-265 | 12 | |
| α-helix | 266-268 | 3 | |
| α-helix | 272-292 | 21 | |
| α-helix | 293-297 | 5 | |
| α-helix | 303-315 | 13 | |
| α-helix | 322-324 | 3 | |
| α-helix | 328-343 | 16 | |
| α-helix | 349-368 | 20 | |
| β-strand | 387-389 | 3 | 15 |
| α-helix | 392-398 | 7 | |
Chain E: 11 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 108 | 1 | 4 |
| β-strand | 114 | 1 | 4 |
| α-helix | 123-125 | 3 | |
| β-strand | 177-179 | 3 | 5 |
| β-strand | 273-274 | 2 | 6 |
| β-strand | 281-282 | 2 | 6 |
| α-helix | 290-292 | 3 | |
| α-helix | 296-298 | 3 | |
| α-helix | 304-311 | 8 | |
| α-helix | 316-329 | 14 | |
| α-helix | 334-336 | 3 | |
| α-helix | 339-342 | 4 | |
| α-helix | 355-358 | 4 | |
| β-strand | 377 | 1 | 7 |
| α-helix | 385-388 | 4 | |
| β-strand | 407 | 1 | 8 |
| β-strand | 414 | 1 | 8 |
| α-helix | 431-433 | 3 | |
| β-strand | 437-439 | 3 | 9 |
| β-strand | 446-448 | 3 | 9 |
| β-strand | 462 | 1 | 7 |
| β-strand | 505-506 | 2 | 10 |
| β-strand | 520-522 | 3 | 10 |
| β-strand | 539-542 | 4 | 10 |
| α-helix | 544-578 | 35 | |
Chain F: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 258-259 | 2 | |
| β-strand | 260-263 | 4 | 16 |
| β-strand | 268 | 1 | 16 |
| β-strand | 272-274 | 3 | 16 |
| β-strand | 280-283 | 4 | 16 |
| α-helix | 284-286 | 3 | |
| α-helix | 290-292 | 3 | |
| α-helix | 296-297 | 2 | |
| α-helix | 304-312 | 9 | |
| α-helix | 316-329 | 14 | |
| α-helix | 334-336 | 3 | |
| α-helix | 337-343 | 7 | |
| α-helix | 346-348 | 3 | |
| β-strand | 364-366 | 3 | 17 |
| β-strand | 372-374 | 3 | 17 |
| α-helix | 544-575 | 32 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transcriptional regulatory protein SIN3 | A | protein | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Transcriptional regulatory protein RCO1 | E, F | protein | 684 | Saccharomyces cerevisiae | Q04779 (AlphaFold model) |
| Histone deacetylase RPD3 | B | protein | 433 | Saccharomyces cerevisiae | P32561 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | C, D | protein | 401 | Saccharomyces cerevisiae | Q12432 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>8W9C_1 Transcriptional regulatory protein SIN3 (chains A)
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 (E, F), FASTA
>8W9C_2 Transcriptional regulatory protein RCO1 (chains E, F)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Sequence of entity 3 (B), FASTA
>8W9C_3 Histone deacetylase RPD3 (chains B)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 4 (C, D), FASTA
>8W9C_4 Chromatin modification-related protein EAF3 (chains C, D)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 7 |
Water and common crystallization additives (K) are not listed.
Primary citation
Structures and dynamics of Rpd3S complex bound to nucleosome. Wang, C., Chu, C., Guo, Z. et al. Sci Adv (2024) 10:eadk7678-eadk7678. DOI 10.1126/sciadv.adk7678 · 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
- 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
Browse structure collections
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