8TOF: Rpd3S
Rpd3S bound to an H3K36Cme3 modified nucleosome. Determined by electron microscopy at 2.8 Å resolution. Released 17 Jan 2024.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organisms
- Saccharomyces cerevisiae, synthetic construct, Xenopus laevis
- Chains
- 18
- Atoms
- 29,102
- Mol. weight
- 713.28 kDa
- Ligands
- ZN
- Released
- 17 Jan 2024
Explore 8TOF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8TOF contains 131 α-helices and 79 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 22 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 23 |
| α-helix | 121-131 | 11 | |
Chain A: 28 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 665-675 | 11 | |
| α-helix | 679-691 | 13 | |
| α-helix | 699-709 | 11 | |
| α-helix | 714-724 | 11 | |
| β-strand | 756-757 | 2 | 1 |
| α-helix | 772-777 | 6 | |
| β-strand | 782-783 | 2 | 1 |
| α-helix | 788-790 | 3 | |
| α-helix | 802-839 | 38 | |
| α-helix | 843-848 | 6 | |
| α-helix | 851-852 | 2 | |
| α-helix | 853-856 | 4 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-884 | 12 | |
| α-helix | 891-927 | 37 | |
| α-helix | 930-933 | 4 | |
| α-helix | 938-942 | 5 | |
| α-helix | 945-964 | 20 | |
| β-strand | 977-978 | 2 | 2 |
| α-helix | 985-998 | 14 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1027-1038 | 12 | |
| β-strand | 1140 | 1 | 3 |
| α-helix | 1142-1172 | 31 | |
| α-helix | 1180-1183 | 4 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1206-1215 | 10 | |
| α-helix | 1221-1229 | 9 | |
| α-helix | 1237-1239 | 3 | |
| α-helix | 1243-1257 | 15 | |
| α-helix | 1261-1273 | 13 | |
| α-helix | 1280-1292 | 13 | |
| β-strand | 1301 | 1 | 3 |
| β-strand | 1304-1306 | 3 | 2 |
| β-strand | 1311-1313 | 3 | 2 |
Chain b: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 23 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 22 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 24 |
Chain B: 17 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 21-24 | 4 | 4 |
| α-helix | 43-54 | 12 | |
| β-strand | 62-66 | 5 | 4 |
| α-helix | 67-69 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-86 | 7 | |
| α-helix | 95-97 | 3 | |
| α-helix | 98-104 | 7 | |
| α-helix | 116-135 | 20 | |
| β-strand | 141-144 | 4 | 4 |
| β-strand | 153 | 1 | 5 |
| β-strand | 156 | 1 | 5 |
| 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 | 203-209 | 7 | 4 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-237 | 5 | 4 |
| α-helix | 244-261 | 18 | |
| β-strand | 267-270 | 4 | 4 |
| α-helix | 273-275 | 3 | |
| α-helix | 288-300 | 13 | |
| β-strand | 305-308 | 4 | 4 |
| α-helix | 317-329 | 13 | |
| α-helix | 333-335 | 3 | |
| β-strand | 337 | 1 | 7 |
| β-strand | 352 | 1 | 7 |
| α-helix | 369-380 | 12 | |
Chain c: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 25 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 26 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 27 |
| α-helix | 113-115 | 3 | |
Chains d and h: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 26 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 25 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
Chain D: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-18 | 6 | 8 |
| β-strand | 21-32 | 12 | 8 |
| β-strand | 37-39 | 3 | 8 |
| β-strand | 59 | 1 | 8 |
| α-helix | 60-62 | 3 | |
| α-helix | 69-72 | 4 | |
| β-strand | 77-81 | 5 | 8 |
| α-helix | 86-88 | 3 | |
| β-strand | 90-92 | 3 | 8 |
| β-strand | 97-98 | 2 | 8 |
| α-helix | 102-130 | 29 | |
| α-helix | 226-239 | 14 | |
| β-strand | 244-246 | 3 | 9 |
| β-strand | 253 | 1 | 10 |
| α-helix | 254-265 | 12 | |
| α-helix | 271-296 | 26 | |
| α-helix | 302-316 | 15 | |
| α-helix | 322-324 | 3 | |
| β-strand | 327 | 1 | 10 |
| α-helix | 328-343 | 16 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-372 | 3 | |
| β-strand | 387-389 | 3 | 9 |
| α-helix | 392-398 | 7 | |
Chain e: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 28 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 29 |
| α-helix | 121-131 | 11 | |
5 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 |
|---|
| Transcriptional regulatory protein SIN3 | A | protein | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Histone deacetylase RPD3 | B | protein | 433 | Saccharomyces cerevisiae | P32561 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | D, E | protein | 401 | Saccharomyces cerevisiae | Q12432 (AlphaFold model) |
| Transcriptional regulatory protein RCO1 | F, G | protein | 684 | Saccharomyces cerevisiae | Q04779 (AlphaFold model) |
| Rco1 | H | protein | 5 | Saccharomyces cerevisiae | |
| DNA (176-mer) | N | DNA | 206 | synthetic construct | |
| DNA (176-mer) | T | DNA | 215 | synthetic construct | |
| Histone H3 | a, e | protein | 136 | Xenopus laevis | P02302 |
| Histone H4 | b, f | protein | 103 | Xenopus laevis | P62799 |
| Histone H2A | c, g | protein | 130 | Xenopus laevis | P06897 |
| Histone H2B 1.1 | d, h | protein | 123 | Xenopus laevis | P02281 |
| histone N-terminal tail | x | protein | 7 | Xenopus laevis | |
Sequence of entity 1 (A), FASTA
>8TOF_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 (B), FASTA
>8TOF_2 Histone deacetylase RPD3 (chains B)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 3 (D, E), FASTA
>8TOF_3 Chromatin modification-related protein EAF3 (chains D, E)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 4 (F, G), FASTA
>8TOF_4 Transcriptional regulatory protein RCO1 (chains F, G)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Sequence of entity 5 (H), FASTA
>8TOF_5 Rco1 (chains H)
XXRXX
Sequence of entity 6 (N), FASTA
>8TOF_6 DNA (176-MER) (chains N)
TTGTGTTTGGTGTGTCTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCAGG
AGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTA
AGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGATATCG
CGCGTGATCTTACGGCATTATACGTA
Sequence of entity 7 (T), FASTA
>8TOF_7 DNA (176-MER) (chains T)
TACGTATAATGCCGTAAGATCACGCGCGATATCAGAATCCCGGTGCCGAGGCCGCTCAAT
TGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAA
CCGCCAAGGGGATTACTCCCTAGTCTCCTGGCACGAGACAGAAAAAAACAACGAAAACGG
CCACCACCCAGACACACCAAACACAAGACAGTGAT
Sequence of entity 8 (a, e), FASTA
>8TOF_8 Histone H3 (chains a, e)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 9 (b, f), FASTA
>8TOF_9 Histone H4 (chains b, f)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 10 (c, g), FASTA
>8TOF_10 Histone H2A (chains c, g)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 11 (d, h), FASTA
>8TOF_11 Histone H2B 1.1 (chains d, h)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 12 (x), FASTA
>8TOF_12 histone N-terminal tail (chains x)
XXXKXXX
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 5 |
Primary citation
Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Markert, J.W., Vos, S.M., Farnung, L. Nat Commun (2023) 14:8128-8128. DOI 10.1038/s41467-023-43968-8 · 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
- 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
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