9V2W: Histone deacetylase complex Rpd3L
Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome. Determined by electron microscopy at 3.4 Å resolution. Released 27 May 2026.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Saccharomyces cerevisiae S288C, Xenopus laevis, synthetic construct
- Chains
- 26
- Atoms
- 39,938
- Mol. weight
- 672.92 kDa
- Ligands
- ZN
- Released
- 27 May 2026
Explore 9V2W in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9V2W contains 157 α-helices and 65 β-strands across 24 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: 38 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 241-250 | 10 | |
| α-helix | 259-267 | 9 | |
| α-helix | 275-282 | 8 | |
| α-helix | 304-309 | 6 | |
| α-helix | 322-330 | 9 | |
| α-helix | 406-414 | 9 | |
| α-helix | 418-421 | 4 | |
| α-helix | 427-439 | 13 | |
| α-helix | 451-454 | 4 | |
| α-helix | 455-457 | 3 | |
| α-helix | 461-468 | 8 | |
| α-helix | 663-672 | 10 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-704 | 6 | |
| α-helix | 707-710 | 4 | |
| β-strand | 755-757 | 3 | 1 |
| β-strand | 782-784 | 3 | 1 |
| α-helix | 802-839 | 38 | |
| α-helix | 843-847 | 5 | |
| α-helix | 863-870 | 8 | |
| α-helix | 873-885 | 13 | |
| α-helix | 887-921 | 35 | |
| α-helix | 924-928 | 5 | |
| α-helix | 930-938 | 9 | |
| α-helix | 940-943 | 4 | |
| α-helix | 945-948 | 4 | |
| β-strand | 976-977 | 2 | 2 |
| α-helix | 984-998 | 15 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1076-1079 | 4 | |
| β-strand | 1135-1140 | 6 | 3 |
| α-helix | 1144-1163 | 20 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1175-1177 | 3 | |
| α-helix | 1179-1182 | 4 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1203-1215 | 13 | |
| α-helix | 1221-1231 | 11 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1273 | 14 | |
| α-helix | 1280-1293 | 14 | |
| α-helix | 1299 | 1 | |
| β-strand | 1300-1306 | 7 | 3 |
| β-strand | 1312-1313 | 2 | 2 |
| β-strand | 1314-1317 | 4 | 3 |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 6 |
Chain C: 17 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 7 |
| α-helix | 43-55 | 13 | |
| α-helix | 57-60 | 4 | |
| β-strand | 62-64 | 3 | 7 |
| α-helix | 67-70 | 4 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-86 | 7 | |
| α-helix | 101-104 | 4 | |
| α-helix | 116-135 | 20 | |
| β-strand | 141-144 | 4 | 7 |
| β-strand | 150 | 1 | 8 |
| β-strand | 152 | 1 | 9 |
| β-strand | 157 | 1 | 9 |
| β-strand | 164 | 1 | 8 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 7 |
| α-helix | 191-194 | 4 | |
| α-helix | 195-197 | 3 | |
| β-strand | 203-207 | 5 | 7 |
| β-strand | 210 | 1 | 10 |
| β-strand | 235 | 1 | 7 |
| β-strand | 238 | 1 | 10 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 7 |
| β-strand | 276 | 1 | 11 |
| β-strand | 286 | 1 | 11 |
| α-helix | 288-291 | 4 | |
| α-helix | 293-299 | 7 | |
| β-strand | 305-308 | 4 | 7 |
| α-helix | 315-329 | 15 | |
| β-strand | 337 | 1 | 12 |
| α-helix | 338-340 | 3 | |
| β-strand | 352 | 1 | 12 |
| α-helix | 366-380 | 15 | |
| α-helix | 381-383 | 3 | |
Chains D and P: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-97 | 10 | |
| α-helix | 101-118 | 18 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 182-190 | 9 | |
| α-helix | 192-209 | 18 | |
| α-helix | 223-291 | 69 | |
| α-helix | 292-294 | 3 | |
Chain F: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-34 | 19 | |
| α-helix | 36-53 | 18 | |
| α-helix | 65-131 | 67 | |
| α-helix | 293-296 | 4 | |
| α-helix | 301-313 | 13 | |
| α-helix | 317-320 | 4 | |
Chain G: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 75-87 | 13 | |
| α-helix | 110-118 | 9 | |
| α-helix | 125-128 | 4 | |
| α-helix | 129-132 | 4 | |
| α-helix | 133-135 | 3 | |
| α-helix | 138-141 | 4 | |
| α-helix | 143-150 | 8 | |
| α-helix | 159-172 | 14 | |
| α-helix | 184-187 | 4 | |
Chain H: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 13 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 14 |
| α-helix | 121-131 | 11 | |
12 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 | 1096 | Saccharomyces cerevisiae S288C | P22579 (AlphaFold model) |
| Histone H2A | B, M, O, S | protein | 107 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone deacetylase RPD3 | C | protein | 378 | Saccharomyces cerevisiae S288C | P32561 (AlphaFold model) |
| Histone H2B | D, N, P, T | protein | 93 | Xenopus laevis | A0A8J1LZU9 (AlphaFold model) |
| Transcriptional regulatory protein DEP1 | E | protein | 119 | Saccharomyces cerevisiae S288C | P31385 |
| Transcriptional regulatory protein SDS3 | F | protein | 311 | Saccharomyces cerevisiae S288C | P40505 |
| Transcriptional regulatory protein SAP30 | G | protein | 119 | Saccharomyces cerevisiae S288C | P38429 |
| Histone H3 | H, Q, U, W | protein | 98 | Xenopus laevis | A0A310TTQ1 |
| Transcriptional regulatory protein PHO23 | I | protein | 105 | Saccharomyces cerevisiae S288C | P50947 |
| Transcriptional regulatory protein RXT2 | J | protein | 206 | Saccharomyces cerevisiae S288C | P38255 |
| Histone deacetylase complex subunit CTI6 | K | protein | 249 | Saccharomyces cerevisiae S288C | Q08923 |
| Histone H4 | L, R, V, Z | protein | 79 | Xenopus laevis | P62799 |
2 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9V2W_1 Transcriptional regulatory protein SIN3 (chains A)
LSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFL
PQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSN
VPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNV
DVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLL
EDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPA
SGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNM
VHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPS
IVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVE
KVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTF
MPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESN
LRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALH
EHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLT
TKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSN
PDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMS
LLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEA
NSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDL
DLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDK
VTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIE
FDKRTLHVSIQYIALD
Sequence of entity 2 (B, M, O, S), FASTA
>9V2W_2 Histone H2A (chains B, M, O, S)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Sequence of entity 3 (C), FASTA
>9V2W_3 Histone deacetylase RPD3 (chains C)
DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKP
ATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSM
EGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVH
HGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYR
SVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVV
GGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEY
LDKVMTNIFANLENTKYA
Sequence of entity 4 (D, N, P, T), FASTA
>9V2W_4 Histone H2B (chains D, N, P, T)
KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sequence of entity 5 (E), FASTA
>9V2W_5 Transcriptional regulatory protein DEP1 (chains E)
EQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDY
KLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRD
Sequence of entity 6 (F), FASTA
>9V2W_6 Transcriptional regulatory protein SDS3 (chains F)
KDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEER
DLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERL
LMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLR
RRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQG
INEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRE
LTGQPPAPFRL
Sequence of entity 7 (G), FASTA
>9V2W_7 Transcriptional regulatory protein SAP30 (chains G)
TAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGY
LLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQ
Sequence of entity 8 (H, Q, U, W), FASTA
>9V2W_8 Histone H3 (chains H, Q, U, W)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 9 (I), FASTA
>9V2W_9 Transcriptional regulatory protein PHO23 (chains I)
LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLN
NINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT
Sequence of entity 10 (J), FASTA
>9V2W_10 Transcriptional regulatory protein RXT2 (chains J)
ILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYE
SNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPF
FALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRN
LQKIRKSVIKANRIRGRILNWSREYL
Sequence of entity 11 (K), FASTA
>9V2W_11 Histone deacetylase complex subunit CTI6 (chains K)
TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLT
EGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTS
ISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQ
RTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLS
MMDDLTREL
Sequence of entity 12 (L, R, V, Z), FASTA
>9V2W_12 Histone H4 (chains L, R, V, Z)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Chromatin context-dependent deacetylation by the asymmetric Rpd3L. Zhao, H., Li, H., Wang, C. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag443 · 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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