8KD5: Rpd3S
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2. Determined by electron microscopy at 2.9 Å resolution. Released 13 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Saccharomyces cerevisiae, Xenopus laevis, synthetic construct
- Chains
- 16
- Atoms
- 26,908
- Mol. weight
- 697.25 kDa
- Ligands
- ZN
- Released
- 13 Sept 2023
Explore 8KD5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8KD5 contains 118 α-helices and 64 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 | 44-54 | 11 | |
| α-helix | 57-60 | 4 | |
| β-strand | 62-64 | 3 | 14 |
| β-strand | 65-66 | 2 | 15 |
| α-helix | 67-69 | 3 | |
| α-helix | 72-74 | 3 | |
| 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 |
| α-helix | 273-275 | 3 | |
| 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 | 366-380 | 15 | |
| α-helix | 405-407 | 3 | |
| β-strand | 413-414 | 2 | 15 |
Chain B: 27 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 | |
| β-strand | 756-757 | 2 | 19 |
| α-helix | 758-759 | 2 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782-783 | 2 | 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 | 974 | 1 | 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 | 1179-1183 | 5 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1229 | 9 | |
| 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 | 1312-1316 | 5 | 20 |
Chain D: 11 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 | 99-111 | 13 | |
| α-helix | 226-236 | 11 | |
| α-helix | 237-241 | 5 | |
| β-strand | 244-245 | 2 | 3 |
| α-helix | 254-268 | 15 | |
| α-helix | 274-292 | 19 | |
| α-helix | 300-315 | 16 | |
| α-helix | 322-324 | 3 | |
| α-helix | 328-342 | 15 | |
| α-helix | 349-368 | 20 | |
| β-strand | 388-389 | 2 | 3 |
| α-helix | 390-391 | 2 | |
| α-helix | 392-399 | 8 | |
Chain E: 12 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-56 | 4 | |
| β-strand | 272-275 | 4 | 21 |
| β-strand | 278-283 | 6 | 21 |
| α-helix | 293-295 | 3 | |
| α-helix | 296-297 | 2 | |
| α-helix | 304-309 | 6 | |
| α-helix | 322-329 | 8 | |
| α-helix | 334-344 | 11 | |
| α-helix | 355-358 | 4 | |
| 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 |
| β-strand | 476-477 | 2 | 26 |
| β-strand | 489-490 | 2 | 26 |
| β-strand | 505-506 | 2 | 27 |
| β-strand | 521-522 | 2 | 28 |
| β-strand | 538-539 | 2 | 27 |
| β-strand | 541-542 | 2 | 28 |
| α-helix | 544-558 | 15 | |
Chain F: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 99-111 | 13 | |
| α-helix | 223-225 | 3 | |
| α-helix | 230-236 | 7 | |
| α-helix | 254-259 | 6 | |
| α-helix | 261-264 | 4 | |
| α-helix | 271 | 1 | |
| α-helix | 276-289 | 14 | |
| α-helix | 300-312 | 13 | |
| α-helix | 330-337 | 8 | |
| α-helix | 339-342 | 4 | |
| α-helix | 349-368 | 20 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 304-311 | 8 | |
| α-helix | 322-328 | 7 | |
| 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 | 1544 | Saccharomyces cerevisiae | P22579 |
| Transcriptional regulatory protein RCO1 | E, G | protein | 684 | Saccharomyces cerevisiae | Q04779 |
Sequence of entity 1 (D, F), FASTA
>8KD5_1 Chromatin modification-related protein EAF3 (chains D, F)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 2 (O, S), FASTA
>8KD5_2 Histone H3 (chains O, S)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 3 (P, T), FASTA
>8KD5_3 Histone H4 (chains P, T)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (Q, U), FASTA
>8KD5_4 Histone H2A (chains Q, U)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 5 (R, V), FASTA
>8KD5_5 Histone H2B 1.1 (chains R, V)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 6 (X), FASTA
>8KD5_6 187bp DNA (chains X)
GCGGTGGCGGCCGCTCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTAT
AGGGTCC
Sequence of entity 7 (Y), FASTA
>8KD5_7 187bp DNA (chains Y)
GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCTAGAGCGGCCG
CCACCGC
Sequence of entity 8 (A), FASTA
>8KD5_8 Histone deacetylase RPD3 (chains A)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 9 (B), FASTA
>8KD5_9 Transcriptional regulatory protein SIN3 (chains B)
MHHHHHHHHSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPS
LSALSTKEEDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSS
SSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQ
RPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVK
FQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIEC
SSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSV
YQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAI
SYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLP
DSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPS
NRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANE
NPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEP
TEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGS
NKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDD
MCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLE
TIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAP
VVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEI
SSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKD
LLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRS
RYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQN
RSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLS
EMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKH
AHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHV
SIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDG
TEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVS
QKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITK
QEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ
Sequence of entity 10 (E, G), FASTA
>8KD5_10 Transcriptional regulatory protein RCO1 (chains E, G)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
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
- 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
- 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
About this viewer
MolViewer shows 8KD5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.