9V2V: Histone deacetylase complex Rpd3L
Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome. Determined by electron microscopy at 3.0 Å resolution. Released 6 May 2026.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Saccharomyces cerevisiae S288C, Xenopus laevis, synthetic construct
- Chains
- 21
- Atoms
- 34,241
- Mol. weight
- 584.44 kDa
- Ligands
- ZN
- Released
- 6 May 2026
Explore 9V2V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9V2V contains 158 α-helices and 71 β-strands across 19 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: 25 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 664-673 | 10 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-710 | 12 | |
| β-strand | 755 | 1 | 1 |
| β-strand | 784 | 1 | 1 |
| α-helix | 804-838 | 35 | |
| α-helix | 843-846 | 4 | |
| α-helix | 862-870 | 9 | |
| α-helix | 876-885 | 10 | |
| α-helix | 887-921 | 35 | |
| α-helix | 924-927 | 4 | |
| α-helix | 930-933 | 4 | |
| α-helix | 935-942 | 8 | |
| β-strand | 977-978 | 2 | 2 |
| α-helix | 983-996 | 14 | |
| α-helix | 1004-1022 | 19 | |
| α-helix | 1076-1079 | 4 | |
| β-strand | 1135 | 1 | 2 |
| β-strand | 1138-1140 | 3 | 2 |
| α-helix | 1145-1162 | 18 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1179-1182 | 4 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1230 | 10 | |
| α-helix | 1237-1241 | 5 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1273 | 14 | |
| α-helix | 1281-1293 | 13 | |
| β-strand | 1300-1306 | 7 | 2 |
| β-strand | 1311-1317 | 7 | 2 |
| α-helix | 1331-1342 | 12 | |
Chain B: 25 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 751 | 1 | 3 |
| β-strand | 753 | 1 | 3 |
| α-helix | 755 | 1 | |
| β-strand | 756 | 1 | 4 |
| β-strand | 783 | 1 | 4 |
| α-helix | 804-813 | 10 | |
| α-helix | 816-824 | 9 | |
| α-helix | 828-838 | 11 | |
| α-helix | 850-852 | 3 | |
| α-helix | 858-860 | 3 | |
| α-helix | 863-870 | 8 | |
| α-helix | 875-877 | 3 | |
| α-helix | 878-885 | 8 | |
| α-helix | 891-914 | 24 | |
| α-helix | 916-919 | 4 | |
| β-strand | 929 | 1 | 5 |
| α-helix | 933-941 | 9 | |
| α-helix | 949-951 | 3 | |
| α-helix | 954-960 | 7 | |
| α-helix | 987-995 | 9 | |
| α-helix | 1005-1007 | 3 | |
| α-helix | 1009-1012 | 4 | |
| α-helix | 1029-1031 | 3 | |
| α-helix | 1142-1145 | 4 | |
| α-helix | 1147-1155 | 9 | |
| α-helix | 1165-1173 | 9 | |
| α-helix | 1189-1192 | 4 | |
| α-helix | 1203-1212 | 10 | |
| α-helix | 1227-1231 | 5 | |
| α-helix | 1252-1255 | 4 | |
| β-strand | 1300-1303 | 4 | 6 |
| β-strand | 1314-1317 | 4 | 6 |
Chain C: 18 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-23 | 3 | 7 |
| β-strand | 24 | 1 | 8 |
| α-helix | 29-31 | 3 | |
| α-helix | 43-54 | 12 | |
| β-strand | 64 | 1 | 8 |
| α-helix | 65-70 | 6 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-86 | 7 | |
| α-helix | 94-96 | 3 | |
| α-helix | 99-102 | 4 | |
| α-helix | 116-135 | 20 | |
| β-strand | 141-144 | 4 | 7 |
| β-strand | 158 | 1 | 9 |
| β-strand | 161 | 1 | 9 |
| α-helix | 165-173 | 9 | |
| β-strand | 180-184 | 5 | 7 |
| α-helix | 193-196 | 4 | |
| β-strand | 203-210 | 8 | 7 |
| β-strand | 234-238 | 5 | 7 |
| α-helix | 244-259 | 16 | |
| β-strand | 266-270 | 5 | 7 |
| β-strand | 276 | 1 | 10 |
| β-strand | 286 | 1 | 10 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 7 |
| α-helix | 315-329 | 15 | |
| α-helix | 338-340 | 3 | |
| α-helix | 344-346 | 3 | |
| α-helix | 366-380 | 15 | |
| α-helix | 381-383 | 3 | |
| α-helix | 384-386 | 3 | |
Chain D: 16 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 11 |
| α-helix | 43-48 | 6 | |
| α-helix | 51-55 | 5 | |
| β-strand | 62-64 | 3 | 11 |
| α-helix | 65-68 | 4 | |
| α-helix | 71-73 | 3 | |
| α-helix | 80-86 | 7 | |
| β-strand | 90 | 1 | 12 |
| β-strand | 93 | 1 | 12 |
| α-helix | 99-102 | 4 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 11 |
| α-helix | 166-172 | 7 | |
| β-strand | 180-183 | 4 | 11 |
| β-strand | 203-210 | 8 | 11 |
| β-strand | 233-238 | 6 | 11 |
| α-helix | 239 | 1 | |
| α-helix | 248-258 | 11 | |
| β-strand | 266-268 | 3 | 11 |
| β-strand | 271 | 1 | 13 |
| α-helix | 289-299 | 11 | |
| β-strand | 305-308 | 4 | 11 |
| β-strand | 309 | 1 | 13 |
| α-helix | 318-329 | 12 | |
| α-helix | 338-340 | 3 | |
| α-helix | 344-347 | 4 | |
| β-strand | 359 | 1 | 5 |
| α-helix | 366-378 | 13 | |
| α-helix | 379-383 | 5 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 178-210 | 33 | |
| α-helix | 214-217 | 4 | |
| α-helix | 227-282 | 56 | |
| α-helix | 285-293 | 9 | |
Chain F: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-17 | 3 | |
| α-helix | 18-34 | 17 | |
| α-helix | 36-51 | 16 | |
| α-helix | 62-122 | 61 | |
| α-helix | 124-140 | 17 | |
| α-helix | 294-297 | 4 | |
| α-helix | 301-314 | 14 | |
| α-helix | 317-320 | 4 | |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 74-87 | 14 | |
| α-helix | 109-119 | 11 | |
| β-strand | 125-126 | 2 | 14 |
| α-helix | 129-132 | 4 | |
| α-helix | 139-141 | 3 | |
| β-strand | 156-157 | 2 | 14 |
| α-helix | 159-170 | 12 | |
Chain H: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 71-75 | 5 | |
| β-strand | 86 | 1 | 15 |
| β-strand | 138 | 1 | 15 |
| β-strand | 140-141 | 2 | 16 |
| β-strand | 144 | 1 | 16 |
| α-helix | 145-152 | 8 | |
| α-helix | 180-183 | 4 | |
| α-helix | 193-196 | 4 | |
| β-strand | 212 | 1 | 16 |
| β-strand | 225-229 | 5 | 16 |
| β-strand | 233 | 1 | 17 |
| β-strand | 264 | 1 | 17 |
| β-strand | 270-273 | 4 | 16 |
10 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, B | protein | 683 | Saccharomyces cerevisiae S288C | P22579 (AlphaFold model) |
| Histone deacetylase RPD3 | C, D | protein | 385 | Saccharomyces cerevisiae S288C | P32561 (AlphaFold model) |
| Transcriptional regulatory protein DEP1 | E | protein | 119 | Saccharomyces cerevisiae S288C | P31385 (AlphaFold model) |
| Transcriptional regulatory protein SDS3 | F | protein | 311 | Saccharomyces cerevisiae S288C | P40505 (AlphaFold model) |
| Transcriptional regulatory protein SAP30 | G | protein | 121 | Saccharomyces cerevisiae S288C | P38429 |
| Transcriptional regulatory protein RXT3 | H | protein | 211 | Saccharomyces cerevisiae S288C | Q07458 |
| Transcriptional regulatory protein PHO23 | I | protein | 105 | Saccharomyces cerevisiae S288C | P50947 |
| Transcriptional regulatory protein RXT2 | J | protein | 218 | Saccharomyces cerevisiae S288C | P38255 |
| Histone deacetylase complex subunit CTI6 | K | protein | 249 | Saccharomyces cerevisiae S288C | Q08923 |
| Histone H2A | O, S | protein | 107 | Xenopus laevis | Q6AZJ8 |
| Histone H2B | P, T | protein | 93 | Xenopus laevis | A0A8J1LZU9 |
| Histone H3 | Q, U | protein | 98 | Xenopus laevis | A0A310TTQ1 |
3 more molecules are not listed.
Sequence of entity 1 (A, B), FASTA
>9V2V_1 Transcriptional regulatory protein SIN3 (chains A, B)
LNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFK
NFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDE
WVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENM
TENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQK
DEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTN
KKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLF
FSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSN
DEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFAN
TNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGE
DAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAK
TAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDD
LTLKEPKADEDKWKYYVTSYALP
Sequence of entity 2 (C, D), FASTA
>9V2V_2 Histone deacetylase RPD3 (chains C, D)
DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKP
ATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSM
EGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVH
HGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYR
SVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVV
GGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEY
LDKVMTNIFANLENTKYAPSVQLNH
Sequence of entity 3 (E), FASTA
>9V2V_3 Transcriptional regulatory protein DEP1 (chains E)
EQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDY
KLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRD
Sequence of entity 4 (F), FASTA
>9V2V_4 Transcriptional regulatory protein SDS3 (chains F)
KDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEER
DLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERL
LMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLR
RRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQG
INEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRE
LTGQPPAPFRL
Sequence of entity 5 (G), FASTA
>9V2V_5 Transcriptional regulatory protein SAP30 (chains G)
RLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQ
GYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKN
Q
Sequence of entity 6 (H), FASTA
>9V2V_6 Transcriptional regulatory protein RXT3 (chains H)
LPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLP
PPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILVLRH
CGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYPSVK
RFDITSREWGSEATVIHDGLSYGIYSIVIKQ
Sequence of entity 7 (I), FASTA
>9V2V_7 Transcriptional regulatory protein PHO23 (chains I)
LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLN
NINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT
Sequence of entity 8 (J), FASTA
>9V2V_8 Transcriptional regulatory protein RXT2 (chains J)
SKLVNVKEILTPILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLE
VFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHIN
NGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQ
IALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYL
Sequence of entity 9 (K), FASTA
>9V2V_9 Histone deacetylase complex subunit CTI6 (chains K)
TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLT
EGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTS
ISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQ
RTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLS
MMDDLTREL
Sequence of entity 10 (O, S), FASTA
>9V2V_10 Histone H2A (chains O, S)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Sequence of entity 11 (P, T), FASTA
>9V2V_11 Histone H2B (chains P, T)
KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sequence of entity 12 (Q, U), FASTA
>9V2V_12 Histone H3 (chains Q, U)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
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
- 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
Browse structure collections
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