8KD4: Rpd3S
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1. Determined by electron microscopy at 2.93 Å resolution. Released 13 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 2.93 Å
- Organisms
- Saccharomyces cerevisiae, Xenopus laevis, synthetic construct
- Chains
- 16
- Atoms
- 27,064
- Mol. weight
- 689.72 kDa
- Ligands
- ZN
- Released
- 13 Sept 2023
Explore 8KD4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8KD4 contains 119 α-helices and 62 β-strands across 14 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: 18 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 14 |
| α-helix | 29-31 | 3 | |
| α-helix | 43-54 | 12 | |
| α-helix | 57-60 | 4 | |
| β-strand | 62-64 | 3 | 14 |
| β-strand | 65 | 1 | 15 |
| α-helix | 66-69 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 91-93 | 3 | |
| α-helix | 99-103 | 5 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 14 |
| β-strand | 158 | 1 | 16 |
| β-strand | 161 | 1 | 16 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 14 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-210 | 8 | 14 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 14 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-272 | 7 | 14 |
| β-strand | 276 | 1 | 17 |
| β-strand | 286 | 1 | 17 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-311 | 7 | 14 |
| α-helix | 316-329 | 14 | |
| β-strand | 337 | 1 | 18 |
| α-helix | 344-346 | 3 | |
| β-strand | 352 | 1 | 18 |
| α-helix | 356-358 | 3 | |
| α-helix | 366-380 | 15 | |
| α-helix | 405-407 | 3 | |
| β-strand | 414 | 1 | 15 |
Chain B: 28 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 665-676 | 12 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-709 | 11 | |
| α-helix | 714-724 | 11 | |
| α-helix | 756 | 1 | |
| β-strand | 757 | 1 | 19 |
| α-helix | 758-759 | 2 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782 | 1 | 19 |
| α-helix | 786-790 | 5 | |
| α-helix | 797-799 | 3 | |
| α-helix | 802-839 | 38 | |
| α-helix | 843-847 | 5 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 891-928 | 38 | |
| α-helix | 935-942 | 8 | |
| α-helix | 945-966 | 22 | |
| β-strand | 977-978 | 2 | 20 |
| α-helix | 983-996 | 14 | |
| α-helix | 1004-1021 | 18 | |
| β-strand | 1136-1140 | 5 | 20 |
| α-helix | 1142-1163 | 22 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1179-1184 | 6 | |
| α-helix | 1203-1215 | 13 | |
| α-helix | 1222-1229 | 8 | |
| α-helix | 1237-1239 | 3 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1272 | 13 | |
| α-helix | 1283-1293 | 11 | |
| β-strand | 1301-1305 | 5 | 20 |
| α-helix | 1308-1310 | 3 | |
| β-strand | 1311-1316 | 6 | 20 |
Chain D: 12 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16 | 1 | 1 |
| β-strand | 23 | 1 | 2 |
| β-strand | 81 | 1 | 2 |
| β-strand | 97 | 1 | 1 |
| α-helix | 99-112 | 14 | |
| α-helix | 226-236 | 11 | |
| α-helix | 237-241 | 5 | |
| β-strand | 244-246 | 3 | 3 |
| α-helix | 254-268 | 15 | |
| α-helix | 274-292 | 19 | |
| α-helix | 302-316 | 15 | |
| α-helix | 322-324 | 3 | |
| α-helix | 328-343 | 16 | |
| α-helix | 349-368 | 20 | |
| β-strand | 387-389 | 3 | 3 |
| α-helix | 390-391 | 2 | |
| α-helix | 392-395 | 4 | |
| α-helix | 396-400 | 5 | |
Chain E: 13 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 52-54 | 3 | |
| β-strand | 272-274 | 3 | 21 |
| β-strand | 281-283 | 3 | 21 |
| α-helix | 293-295 | 3 | |
| α-helix | 296-298 | 3 | |
| α-helix | 304-307 | 4 | |
| α-helix | 322-329 | 8 | |
| α-helix | 334-344 | 11 | |
| α-helix | 355-359 | 5 | |
| β-strand | 365-366 | 2 | 22 |
| β-strand | 372-373 | 2 | 22 |
| β-strand | 377 | 1 | 23 |
| α-helix | 378-382 | 5 | |
| α-helix | 383-386 | 4 | |
| α-helix | 403-406 | 4 | |
| β-strand | 407 | 1 | 24 |
| β-strand | 414 | 1 | 24 |
| α-helix | 431-433 | 3 | |
| β-strand | 437-438 | 2 | 25 |
| β-strand | 447-448 | 2 | 25 |
| β-strand | 462 | 1 | 23 |
| α-helix | 470-471 | 2 | |
| β-strand | 476-477 | 2 | 26 |
| β-strand | 489-490 | 2 | 26 |
| β-strand | 521-522 | 2 | 27 |
| β-strand | 541-542 | 2 | 27 |
| α-helix | 544-558 | 15 | |
Chain F: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 99-111 | 13 | |
| α-helix | 223-225 | 3 | |
| α-helix | 230-238 | 9 | |
| α-helix | 254-259 | 6 | |
| α-helix | 261-264 | 4 | |
| α-helix | 271 | 1 | |
| α-helix | 276-289 | 14 | |
| α-helix | 300-313 | 14 | |
| α-helix | 329-342 | 14 | |
| α-helix | 349-366 | 18 | |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 323-325 | 3 | |
| α-helix | 338-341 | 4 | |
| α-helix | 542-568 | 27 | |
Chain O: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 4 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 5 |
| α-helix | 121-131 | 11 | |
Chains P and T: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 5 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 4 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 6 |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromatin modification-related protein EAF3 | D, F | protein | 401 | Saccharomyces cerevisiae | Q12432 (AlphaFold model) |
| Histone H3 | O, S | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | P, T | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | Q, U | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | R, V | protein | 122 | Xenopus laevis | P02281 |
| 187bp DNA | X | DNA | 187 | synthetic construct | |
| 187bp DNA | Y | DNA | 187 | synthetic construct | |
| Histone deacetylase RPD3 | A | protein | 433 | Saccharomyces cerevisiae | P32561 |
| Transcriptional regulatory protein SIN3 | B | protein | 1371 | Saccharomyces cerevisiae | P22579 |
| Transcriptional regulatory protein RCO1 | E, G | protein | 733 | Saccharomyces cerevisiae | Q04779 |
Sequence of entity 1 (D, F), FASTA
>8KD4_1 Chromatin modification-related protein EAF3 (chains D, F)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 2 (O, S), FASTA
>8KD4_2 Histone H3 (chains O, S)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 3 (P, T), FASTA
>8KD4_3 Histone H4 (chains P, T)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (Q, U), FASTA
>8KD4_4 Histone H2A (chains Q, U)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 5 (R, V), FASTA
>8KD4_5 Histone H2B 1.1 (chains R, V)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 6 (X), FASTA
>8KD4_6 187bp DNA (chains X)
GCGGTGGCGGCCGCTCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTAT
AGGGTCC
Sequence of entity 7 (Y), FASTA
>8KD4_7 187bp DNA (chains Y)
GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCTAGAGCGGCCG
CCACCGC
Sequence of entity 8 (A), FASTA
>8KD4_8 Histone deacetylase RPD3 (chains A)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 9 (B), FASTA
>8KD4_9 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 10 (E, G), FASTA
>8KD4_10 Transcriptional regulatory protein RCO1 (chains E, G)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSEMHHHHHHHHPQLAMWSHPQFEKGGGSGGGSGGGSWS
HPQFEKENLYFQS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
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 Q12432 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
- 3E9F 1.8 Å, Crystal structure short-form (residue1-113) of Eaf3 chromo domain
- 8I3G 2.4 Å, Crystal structure of Eaf3-Eaf7 complex
- 3E9G 2.5 Å, Crystal structure long-form (residue1-124) of Eaf3 chromo domain
- 7YI1 2.8 Å, Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome
- 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
- 8HXX 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S
- 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
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