8IHN: Rpd3S core complex
Cryo-EM structure of the Rpd3S core complex. Determined by electron microscopy at 3.37 Å resolution. Released 20 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.37 Å
- Organisms
- Xenopus laevis, Saccharomyces cerevisiae
- Chains
- 7
- Atoms
- 14,611
- Mol. weight
- 475.11 kDa
- Ligands
- CA, ZN
- Released
- 20 Mar 2024
Explore 8IHN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IHN contains 100 α-helices and 45 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 K: 32 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 661-665 | 5 | |
| α-helix | 668-676 | 9 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-710 | 12 | |
| α-helix | 714-724 | 11 | |
| β-strand | 756-757 | 2 | 1 |
| α-helix | 758-759 | 2 | |
| α-helix | 761-764 | 4 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782-783 | 2 | 1 |
| α-helix | 786-789 | 4 | |
| α-helix | 797-799 | 3 | |
| α-helix | 806-840 | 35 | |
| α-helix | 843-847 | 5 | |
| α-helix | 853-856 | 4 | |
| α-helix | 862-870 | 9 | |
| α-helix | 875-885 | 11 | |
| α-helix | 887-928 | 42 | |
| α-helix | 930-933 | 4 | |
| α-helix | 935-942 | 8 | |
| α-helix | 947-964 | 18 | |
| β-strand | 975-978 | 4 | 2 |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1026-1039 | 14 | |
| α-helix | 1065-1068 | 4 | |
| α-helix | 1071-1079 | 9 | |
| β-strand | 1129 | 1 | 3 |
| β-strand | 1136-1140 | 5 | 2 |
| α-helix | 1142-1174 | 33 | |
| α-helix | 1179-1182 | 4 | |
| α-helix | 1190-1194 | 5 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1232 | 12 | |
| α-helix | 1242-1257 | 16 | |
| α-helix | 1260-1274 | 15 | |
| β-strand | 1279 | 1 | 3 |
| α-helix | 1280-1293 | 14 | |
| β-strand | 1301-1306 | 6 | 2 |
| β-strand | 1311-1316 | 6 | 2 |
Chain L: 20 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 4 |
| α-helix | 27-31 | 5 | |
| α-helix | 43-54 | 12 | |
| α-helix | 57-59 | 3 | |
| β-strand | 63-64 | 2 | 4 |
| α-helix | 66-70 | 5 | |
| α-helix | 73-76 | 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 | 4 |
| β-strand | 158 | 1 | 5 |
| β-strand | 161 | 1 | 5 |
| α-helix | 165-173 | 9 | |
| β-strand | 180-184 | 5 | 4 |
| α-helix | 191-194 | 4 | |
| β-strand | 203-210 | 8 | 4 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 4 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 4 |
| β-strand | 276 | 1 | 6 |
| β-strand | 286 | 1 | 6 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 4 |
| α-helix | 315-329 | 15 | |
| α-helix | 333-335 | 3 | |
| α-helix | 338-340 | 3 | |
| α-helix | 360-362 | 3 | |
| α-helix | 366-380 | 15 | |
| α-helix | 410-413 | 4 | |
Chain M: 18 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 87 | 1 | 7 |
| α-helix | 92 | 1 | |
| β-strand | 93 | 1 | 7 |
| α-helix | 94-95 | 2 | |
| α-helix | 113-114 | 2 | |
| β-strand | 272-274 | 3 | 8 |
| β-strand | 281-283 | 3 | 8 |
| α-helix | 304-312 | 9 | |
| α-helix | 319-329 | 11 | |
| α-helix | 334-336 | 3 | |
| α-helix | 337-342 | 6 | |
| α-helix | 347-348 | 2 | |
| α-helix | 355-358 | 4 | |
| β-strand | 365-366 | 2 | 9 |
| β-strand | 372-373 | 2 | 9 |
| α-helix | 378-382 | 5 | |
| α-helix | 383-387 | 5 | |
| α-helix | 403-405 | 3 | |
| α-helix | 414-415 | 2 | |
| α-helix | 425-427 | 3 | |
| α-helix | 431-433 | 3 | |
| β-strand | 437-439 | 3 | 10 |
| β-strand | 446-448 | 3 | 10 |
| α-helix | 465-466 | 2 | |
| β-strand | 473-477 | 5 | 11 |
| β-strand | 489-493 | 5 | 11 |
| α-helix | 494-499 | 6 | |
| β-strand | 504-506 | 3 | 12 |
| β-strand | 520-523 | 4 | 12 |
| β-strand | 538-543 | 6 | 12 |
| α-helix | 544-576 | 33 | |
Chain N: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-240 | 15 | |
| β-strand | 244-246 | 3 | 13 |
| β-strand | 253 | 1 | 14 |
| α-helix | 254-268 | 15 | |
| α-helix | 272-296 | 25 | |
| α-helix | 300-302 | 3 | |
| α-helix | 303-316 | 14 | |
| α-helix | 322-325 | 4 | |
| β-strand | 327 | 1 | 14 |
| α-helix | 328-336 | 9 | |
| α-helix | 338-344 | 7 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-373 | 4 | |
| β-strand | 387-389 | 3 | 13 |
| α-helix | 392-399 | 8 | |
Chain O: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 262-263 | 2 | 15 |
| β-strand | 268-269 | 2 | 15 |
| β-strand | 272-274 | 3 | 16 |
| β-strand | 281-283 | 3 | 16 |
| α-helix | 304-312 | 9 | |
| α-helix | 316-329 | 14 | |
| α-helix | 338-343 | 6 | |
| α-helix | 347-348 | 2 | |
| α-helix | 355-360 | 6 | |
| α-helix | 544-576 | 33 | |
Chain P: 13 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-237 | 12 | |
| α-helix | 238-242 | 5 | |
| β-strand | 245-246 | 2 | 17 |
| β-strand | 253 | 1 | 18 |
| α-helix | 254-264 | 11 | |
| α-helix | 265-267 | 3 | |
| α-helix | 272-292 | 21 | |
| α-helix | 293-297 | 5 | |
| α-helix | 300-316 | 17 | |
| α-helix | 319-320 | 2 | |
| α-helix | 322-325 | 4 | |
| β-strand | 327 | 1 | 18 |
| α-helix | 328-344 | 17 | |
| α-helix | 349-369 | 21 | |
| α-helix | 370-374 | 5 | |
| β-strand | 387-388 | 2 | 17 |
| α-helix | 392-399 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A | protein | 24 | Xenopus laevis | P84233 (AlphaFold model) |
| Transcriptional regulatory protein SIN3 | K | protein | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Histone deacetylase RPD3 | L | protein | 433 | Saccharomyces cerevisiae | P32561 (AlphaFold model) |
| RCO1 isoform 1 | M, O | protein | 684 | Saccharomyces cerevisiae | Q04779 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | N, P | protein | 401 | Saccharomyces cerevisiae | Q12432 |
Sequence of entity 1 (A), FASTA
>8IHN_1 Histone H3 (chains A)
ARTKQTARKSTGGKAPRKQLATKA
Sequence of entity 2 (K), FASTA
>8IHN_2 Transcriptional regulatory protein SIN3 (chains K)
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 3 (L), FASTA
>8IHN_3 Histone deacetylase RPD3 (chains L)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 4 (M, O), FASTA
>8IHN_4 RCO1 isoform 1 (chains M, O)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Sequence of entity 5 (N, P), FASTA
>8IHN_5 Chromatin modification-related protein EAF3 (chains N, P)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 1 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Zhang, Y., Xu, M., Wang, P. et al. Cell Res (2023) 33:971-974. DOI 10.1038/s41422-023-00884-2 · PubMed
Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
Browse structure collections
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