7YI2: Rpd3S in loose-state Rpd3S-NCP complex
Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex. Determined by electron microscopy at 3.4 Å resolution. Released 14 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- synthetic construct, Saccharomyces cerevisiae S288C
- Chains
- 7
- Atoms
- 12,140
- Mol. weight
- 530.61 kDa
- Ligands
- ZN
- Released
- 14 Jun 2023
Explore 7YI2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YI2 contains 66 α-helices and 36 β-strands across 5 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: 27 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 668-676 | 9 | |
| α-helix | 680-693 | 14 | |
| α-helix | 700-710 | 11 | |
| α-helix | 716-724 | 9 | |
| α-helix | 760-763 | 4 | |
| α-helix | 772-777 | 6 | |
| α-helix | 786-789 | 4 | |
| α-helix | 802-838 | 37 | |
| α-helix | 862-870 | 9 | |
| α-helix | 876-884 | 9 | |
| α-helix | 891-920 | 30 | |
| α-helix | 924-927 | 4 | |
| α-helix | 931-934 | 4 | |
| α-helix | 938-942 | 5 | |
| α-helix | 945-959 | 15 | |
| β-strand | 975-978 | 4 | 1 |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1028-1030 | 3 | |
| β-strand | 1135-1136 | 2 | 1 |
| β-strand | 1139-1140 | 2 | 1 |
| α-helix | 1142-1163 | 22 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1182-1185 | 4 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1232 | 12 | |
| α-helix | 1237-1239 | 3 | |
| α-helix | 1242-1257 | 16 | |
| α-helix | 1260-1275 | 16 | |
| α-helix | 1282-1293 | 12 | |
| β-strand | 1300-1306 | 7 | 1 |
| β-strand | 1311-1317 | 7 | 1 |
Chain B: 19 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21 | 1 | 2 |
| β-strand | 22-24 | 3 | 3 |
| α-helix | 43-53 | 11 | |
| α-helix | 57-59 | 3 | |
| β-strand | 62-66 | 5 | 3 |
| α-helix | 67-69 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-86 | 7 | |
| α-helix | 99-104 | 6 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 2 |
| β-strand | 158 | 1 | 4 |
| β-strand | 161 | 1 | 4 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 2 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-210 | 8 | 2 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 2 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 2 |
| α-helix | 273-275 | 3 | |
| β-strand | 276 | 1 | 5 |
| β-strand | 286 | 1 | 5 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 2 |
| α-helix | 315-329 | 15 | |
| α-helix | 333-335 | 3 | |
| β-strand | 337 | 1 | 6 |
| α-helix | 345-347 | 3 | |
| β-strand | 352 | 1 | 6 |
| α-helix | 356-358 | 3 | |
| α-helix | 360-362 | 3 | |
| α-helix | 366-380 | 15 | |
Chain C: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-240 | 15 | |
| β-strand | 245-246 | 2 | 7 |
| α-helix | 254-266 | 13 | |
| α-helix | 273-296 | 24 | |
| α-helix | 303-314 | 12 | |
| α-helix | 322-324 | 3 | |
| α-helix | 338-342 | 5 | |
| α-helix | 350-368 | 19 | |
| β-strand | 387-388 | 2 | 7 |
| α-helix | 392-400 | 9 | |
Chain D: 11 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 121-126 | 6 | |
| α-helix | 169-172 | 4 | |
| β-strand | 177-179 | 3 | 3 |
| β-strand | 273-274 | 2 | 8 |
| β-strand | 281-282 | 2 | 8 |
| α-helix | 304-311 | 8 | |
| α-helix | 318-327 | 10 | |
| α-helix | 337-342 | 6 | |
| α-helix | 358-360 | 3 | |
| β-strand | 364-366 | 3 | 9 |
| β-strand | 372-374 | 3 | 9 |
| α-helix | 404-406 | 3 | |
| β-strand | 407 | 1 | 10 |
| β-strand | 414 | 1 | 10 |
| α-helix | 431-433 | 3 | |
| β-strand | 437 | 1 | 11 |
| β-strand | 448 | 1 | 11 |
| β-strand | 473-476 | 4 | 12 |
| β-strand | 490-493 | 4 | 12 |
| α-helix | 494-497 | 4 | |
| β-strand | 505-506 | 2 | 13 |
| β-strand | 520-521 | 2 | 13 |
| α-helix | 538 | 1 | |
| β-strand | 539-541 | 3 | 13 |
| α-helix | 545-563 | 19 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 547-562 | 16 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Wisdom 601 DNA (167-MER) | G | DNA | 167 | synthetic construct | |
| Wisdom 601 DNA (167-MER) | H | DNA | 167 | synthetic construct | |
| Transcriptional regulatory protein SIN3 | A | protein | 1536 | Saccharomyces cerevisiae S288C | P22579 (AlphaFold model) |
| Histone deacetylase RPD3 | B | protein | 433 | Saccharomyces cerevisiae S288C | P32561 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | C | protein | 401 | Saccharomyces cerevisiae S288C | Q12432 (AlphaFold model) |
| Transcriptional regulatory protein RCO1 | D, E | protein | 684 | Saccharomyces cerevisiae S288C | Q04779 (AlphaFold model) |
Sequence of entity 1 (G), FASTA
>7YI2_1 Wisdom 601 DNA (167-MER) (chains G)
CTGGAGAATCCCGGTCTGCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACC
Sequence of entity 2 (H), FASTA
>7YI2_2 Wisdom 601 DNA (167-MER) (chains H)
GGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTGCAGACCGGGATTCTCCAG
Sequence of entity 3 (A), FASTA
>7YI2_3 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 4 (B), FASTA
>7YI2_4 Histone deacetylase RPD3 (chains B)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 5 (C), FASTA
>7YI2_5 Chromatin modification-related protein EAF3 (chains C)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 6 (D, E), FASTA
>7YI2_6 Transcriptional regulatory protein RCO1 (chains D, E)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 5 |
Primary citation
Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S. Guan, H., Wang, P., Zhang, P. et al. Nature (2023) 620:669-675. DOI 10.1038/s41586-023-06349-1 · 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
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