8GA8: Yeast (HDAC) Rpd3L complex
Structure of the yeast (HDAC) Rpd3L complex. Determined by electron microscopy at 3.5 Å resolution. Released 12 Jul 2023.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 10
- Atoms
- 22,011
- Mol. weight
- 675.55 kDa
- Ligands
- ZN
- Released
- 12 Jul 2023
Explore 8GA8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8GA8 contains 134 α-helices and 67 β-strands across 10 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: 28 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 660-676 | 17 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-706 | 8 | |
| α-helix | 714-723 | 10 | |
| β-strand | 750-751 | 2 | 1 |
| β-strand | 755-757 | 3 | 1 |
| α-helix | 758-759 | 2 | |
| α-helix | 760-763 | 4 | |
| α-helix | 773-776 | 4 | |
| β-strand | 782-783 | 2 | 1 |
| α-helix | 804-838 | 35 | |
| α-helix | 843-845 | 3 | |
| α-helix | 851-852 | 2 | |
| α-helix | 862-870 | 9 | |
| α-helix | 876-885 | 10 | |
| α-helix | 887-921 | 35 | |
| α-helix | 924-928 | 5 | |
| β-strand | 929 | 1 | 2 |
| α-helix | 935-942 | 8 | |
| α-helix | 945-960 | 16 | |
| β-strand | 976-978 | 3 | 3 |
| α-helix | 984-998 | 15 | |
| α-helix | 1004-1022 | 19 | |
| α-helix | 1066-1069 | 4 | |
| α-helix | 1071-1081 | 11 | |
| β-strand | 1136-1140 | 5 | 3 |
| α-helix | 1142-1162 | 21 | |
| α-helix | 1165-1174 | 10 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1203-1215 | 13 | |
| α-helix | 1221-1232 | 12 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1273 | 14 | |
| α-helix | 1280-1293 | 14 | |
| β-strand | 1301-1305 | 5 | 3 |
| β-strand | 1311-1316 | 6 | 3 |
Chain B: 18 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 21-24 | 4 | 8 |
| α-helix | 29-31 | 3 | |
| α-helix | 43-54 | 12 | |
| α-helix | 57-60 | 4 | |
| β-strand | 62-64 | 3 | 8 |
| α-helix | 66-70 | 5 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 98-104 | 7 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141 | 1 | 8 |
| β-strand | 144 | 1 | 8 |
| β-strand | 152 | 1 | 9 |
| β-strand | 157 | 1 | 9 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-183 | 4 | 8 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-206 | 4 | 8 |
| β-strand | 210 | 1 | 10 |
| α-helix | 227-229 | 3 | |
| β-strand | 238 | 1 | 10 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 8 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 8 |
| α-helix | 316-328 | 13 | |
| α-helix | 333-335 | 3 | |
| β-strand | 337 | 1 | 11 |
| α-helix | 344-346 | 3 | |
| β-strand | 352 | 1 | 11 |
| β-strand | 359 | 1 | 2 |
| α-helix | 366-380 | 15 | |
Chain D: 29 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 663-676 | 14 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-709 | 11 | |
| α-helix | 714-723 | 10 | |
| β-strand | 750 | 1 | 20 |
| β-strand | 755-757 | 3 | 20 |
| α-helix | 758-759 | 2 | |
| α-helix | 761-763 | 3 | |
| α-helix | 772-777 | 6 | |
| β-strand | 782-784 | 3 | 20 |
| α-helix | 799-801 | 3 | |
| α-helix | 802-840 | 39 | |
| α-helix | 843-847 | 5 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 887-923 | 37 | |
| α-helix | 930-942 | 13 | |
| α-helix | 945-955 | 11 | |
| α-helix | 956-960 | 5 | |
| α-helix | 969-971 | 3 | |
| β-strand | 975-978 | 4 | 21 |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1022 | 19 | |
| α-helix | 1066-1069 | 4 | |
| β-strand | 1130 | 1 | 22 |
| β-strand | 1135-1140 | 6 | 21 |
| α-helix | 1142-1159 | 18 | |
| α-helix | 1161-1163 | 3 | |
| α-helix | 1165-1172 | 8 | |
| α-helix | 1204-1215 | 12 | |
| α-helix | 1221-1231 | 11 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1273 | 14 | |
| β-strand | 1278 | 1 | 22 |
| α-helix | 1280-1292 | 13 | |
| α-helix | 1299-1300 | 2 | |
| β-strand | 1301-1306 | 6 | 21 |
| β-strand | 1311-1316 | 6 | 21 |
Chain E: 18 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 12 |
| α-helix | 29-31 | 3 | |
| α-helix | 43-55 | 13 | |
| β-strand | 62-64 | 3 | 12 |
| α-helix | 66-70 | 5 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 98-104 | 7 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 12 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-183 | 4 | 12 |
| α-helix | 191-195 | 5 | |
| β-strand | 203-205 | 3 | 12 |
| β-strand | 207 | 1 | 13 |
| β-strand | 210 | 1 | 14 |
| α-helix | 227-229 | 3 | |
| β-strand | 235 | 1 | 13 |
| β-strand | 238 | 1 | 14 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 12 |
| β-strand | 276 | 1 | 15 |
| β-strand | 286 | 1 | 15 |
| α-helix | 288-299 | 12 | |
| β-strand | 305-308 | 4 | 12 |
| α-helix | 315-329 | 15 | |
| α-helix | 338-340 | 3 | |
| α-helix | 344-346 | 3 | |
| α-helix | 356-358 | 3 | |
| α-helix | 360-362 | 3 | |
| α-helix | 366-380 | 15 | |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 222-297 | 76 | |
| α-helix | 395-403 | 9 | |
Chain H: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-34 | 23 | |
| α-helix | 36-55 | 20 | |
| α-helix | 60-116 | 57 | |
| α-helix | 292-297 | 6 | |
| α-helix | 301-315 | 15 | |
| α-helix | 317-321 | 5 | |
Chain J: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 109-119 | 11 | |
| α-helix | 124-125 | 2 | |
| β-strand | 126 | 1 | 4 |
| α-helix | 127-128 | 2 | |
| α-helix | 129-134 | 6 | |
| α-helix | 139-141 | 3 | |
| α-helix | 143-147 | 5 | |
| β-strand | 157 | 1 | 4 |
| α-helix | 159-172 | 14 | |
| α-helix | 177-190 | 14 | |
Chain K: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 71-79 | 9 | |
| α-helix | 82-84 | 3 | |
| β-strand | 86 | 1 | 16 |
| β-strand | 90-91 | 2 | 16 |
| α-helix | 132-134 | 3 | |
| β-strand | 138-143 | 6 | 16 |
| α-helix | 145-152 | 8 | |
| α-helix | 158-162 | 5 | |
| β-strand | 166 | 1 | 17 |
| β-strand | 167 | 1 | 16 |
| β-strand | 171-172 | 2 | 16 |
| α-helix | 177-183 | 7 | |
| α-helix | 191-192 | 2 | |
| β-strand | 212-213 | 2 | 16 |
| β-strand | 225-233 | 9 | 16 |
| α-helix | 234-236 | 3 | |
| β-strand | 239 | 1 | 18 |
| β-strand | 243-244 | 2 | 19 |
| β-strand | 247-248 | 2 | 19 |
| α-helix | 249 | 1 | |
| β-strand | 250 | 1 | 17 |
| α-helix | 251 | 1 | |
| β-strand | 252 | 1 | 18 |
| β-strand | 264-273 | 10 | 16 |
2 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 SDS3 | H | protein | 327 | Saccharomyces cerevisiae | P40505 (AlphaFold model) |
| Transcriptional regulatory protein SIN3 | A, D | protein | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Transcriptional regulatory protein SAP30 | J | protein | 201 | Saccharomyces cerevisiae | P38429 (AlphaFold model) |
| Transcriptional regulatory protein PHO23 | L | protein | 330 | Saccharomyces cerevisiae | P50947 (AlphaFold model) |
| Transcriptional regulatory protein RXT2 | M | protein | 430 | Saccharomyces cerevisiae | P38255 |
| Transcriptional regulatory protein DEP1 | G | protein | 405 | Saccharomyces cerevisiae | P31385 |
| Histone deacetylase RPD3 | B, E | protein | 433 | Saccharomyces cerevisiae | P32561 |
| Transcriptional regulatory protein RXT3 | K | protein | 294 | Saccharomyces cerevisiae | Q07458 |
Sequence of entity 1 (H), FASTA
>8GA8_1 Transcriptional regulatory protein SDS3 (chains H)
MAIQKVSNKDLSRKDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNG
QYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSS
IEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESA
TDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTY
KSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLK
PDEVTEDISLIRELTGQPPAPFRLRSD
Sequence of entity 2 (A, D), FASTA
>8GA8_2 Transcriptional regulatory protein SIN3 (chains A, D)
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 (J), FASTA
>8GA8_3 Transcriptional regulatory protein SAP30 (chains J)
MARPVNTNAETESRGRPTQGGGYASNNNGSCNNNNGSNNNNNNNNNNNNNSNNSNNNNGP
TSSGRTNGKQRLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQ
LDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDC
IPQFIYKVKNQKKKFKMEFRG
Sequence of entity 4 (L), FASTA
>8GA8_4 Transcriptional regulatory protein PHO23 (chains L)
MSSPANLFPGLNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNK
DHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNTEIPRG
LRLGVDNHPAMHLHHELMEKIESKSNSKSSQALKSESRREAMAANRRQGEHYSASTHQQD
DSKNDANYGGSRHESQDHTGNNTNSRKRANAANTNNADPETKKRKRRVATTAVSPSTIST
ATAVNNGRIGTSTASRGVSSVGNSNNSRISRPKTNDYGEPLYCYCNQVAYGEMVGCDGAD
CELEWFHLPCIGLETLPKGKWYCDDCKKKL
Sequence of entity 5 (M), FASTA
>8GA8_5 Transcriptional regulatory protein RXT2 (chains M)
MTIRSSMKNNAELESKSVLANESNIISTFTRRIIKEKSGNYQVLKRSLDGKLIYPEATGI
SSNRGNKLLQRSEVVTRRDLNNSKPMIEQTVFYNGSEHRLLQTNIVTDSRRKRIKFTPDI
NVEPVLVGDENDIDGSEKEDENITDEYYGEEDDDDLSKLVNVKEILTPILSLGDIINHKT
ISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNL
TLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNAL
LSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKAN
RIRGRILNWSREYLGISDDDITIPVALRVVKRGLISATTNKTTNFEEEIENTMEDGVVDD
NEPDEEANRA
Sequence of entity 6 (G), FASTA
>8GA8_6 Transcriptional regulatory protein DEP1 (chains G)
MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEK
SLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKS
QELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRM
TALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHR
AYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVI
PDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIV
DRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQ
Sequence of entity 7 (B, E), FASTA
>8GA8_7 Histone deacetylase RPD3 (chains B, E)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 8 (K), FASTA
>8GA8_8 Transcriptional regulatory protein RXT3 (chains K)
MSVSEQDPNRAYRETQSQIYKLQETLLNSARTKNKQEEGQESNTHSFPEQYMHYQNGRNS
AYDLPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDN
TLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILV
LRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYP
SVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQRLDRDKPHEPNGYIKNLKWT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Patel, A.B., Qing, J., Tam, K.H. et al. Nat Commun (2023) 14:3061-3061. DOI 10.1038/s41467-023-38687-z · PubMed
Other PDB entries of the same protein (UniProt P40505 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8HPO 2.6 Å, Cryo-EM structure of a SIN3/HDAC complex from budding yeast
- 9V2V 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
- 9V2W 3.4 Å, Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome
Browse structure collections
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