8W9E: Transcriptional regulatory protein SIN3
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2. Determined by electron microscopy at 3.6 Å resolution. Released 15 May 2024.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Saccharomyces cerevisiae, Homo sapiens
- Chains
- 17
- Atoms
- 27,886
- Mol. weight
- 718.77 kDa
- Ligands
- ZN
- Released
- 15 May 2024
Explore 8W9E in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8W9E contains 125 α-helices and 72 β-strands across 15 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 20 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 21 |
| α-helix | 121-131 | 11 | |
Chain A: 30 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 664-675 | 12 | |
| α-helix | 679-693 | 15 | |
| α-helix | 699-710 | 12 | |
| α-helix | 714-724 | 11 | |
| α-helix | 773-777 | 5 | |
| α-helix | 802-839 | 38 | |
| α-helix | 843-848 | 6 | |
| α-helix | 862-870 | 9 | |
| α-helix | 873-885 | 13 | |
| α-helix | 887-921 | 35 | |
| α-helix | 925-927 | 3 | |
| α-helix | 945-963 | 19 | |
| α-helix | 971-973 | 3 | |
| β-strand | 975-978 | 4 | 1 |
| α-helix | 983-998 | 16 | |
| α-helix | 1004-1021 | 18 | |
| α-helix | 1026-1038 | 13 | |
| α-helix | 1065-1069 | 5 | |
| α-helix | 1071-1080 | 10 | |
| α-helix | 1119-1126 | 8 | |
| β-strand | 1135-1136 | 2 | 1 |
| β-strand | 1139-1140 | 2 | 1 |
| α-helix | 1142-1173 | 32 | |
| α-helix | 1179-1183 | 5 | |
| α-helix | 1190-1193 | 4 | |
| α-helix | 1203-1216 | 14 | |
| α-helix | 1221-1231 | 11 | |
| α-helix | 1238-1241 | 4 | |
| α-helix | 1242-1258 | 17 | |
| α-helix | 1260-1274 | 15 | |
| α-helix | 1280-1291 | 12 | |
| β-strand | 1300-1306 | 7 | 1 |
| β-strand | 1311-1317 | 7 | 1 |
| α-helix | 1325-1327 | 3 | |
| α-helix | 1330-1342 | 13 | |
Chain b: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 46 | 1 | 21 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 20 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 22 |
Chain B: 17 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 22-24 | 3 | 12 |
| α-helix | 44-54 | 11 | |
| β-strand | 62-64 | 3 | 12 |
| β-strand | 66 | 1 | 2 |
| α-helix | 67-70 | 4 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 94-97 | 4 | |
| α-helix | 100-103 | 4 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141-144 | 4 | 12 |
| α-helix | 165-174 | 10 | |
| β-strand | 180-184 | 5 | 12 |
| α-helix | 191-196 | 6 | |
| β-strand | 203-210 | 8 | 12 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-238 | 6 | 12 |
| α-helix | 244-261 | 18 | |
| β-strand | 266-270 | 5 | 12 |
| β-strand | 276 | 1 | 13 |
| β-strand | 286 | 1 | 13 |
| α-helix | 289-300 | 12 | |
| β-strand | 305-308 | 4 | 12 |
| α-helix | 315-329 | 15 | |
| α-helix | 333-335 | 3 | |
| β-strand | 337 | 1 | 14 |
| β-strand | 352 | 1 | 14 |
| α-helix | 360-362 | 3 | |
| α-helix | 366-380 | 15 | |
Chain c: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 23 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 24 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 25 |
Chain C: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-238 | 13 | |
| β-strand | 244-246 | 3 | 15 |
| α-helix | 254-268 | 15 | |
| α-helix | 272-296 | 25 | |
| α-helix | 303-316 | 14 | |
| α-helix | 322-324 | 3 | |
| α-helix | 329-343 | 15 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-373 | 4 | |
| β-strand | 387-389 | 3 | 15 |
| α-helix | 392-400 | 9 | |
Chains d and h: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 24 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 23 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain D: 12 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 226-240 | 15 | |
| β-strand | 244-246 | 3 | 16 |
| α-helix | 250 | 1 | |
| α-helix | 254-265 | 12 | |
| α-helix | 266-268 | 3 | |
| α-helix | 272-292 | 21 | |
| α-helix | 303-316 | 14 | |
| α-helix | 329-343 | 15 | |
| α-helix | 349-368 | 20 | |
| α-helix | 370-374 | 5 | |
| α-helix | 382-384 | 3 | |
| β-strand | 387-389 | 3 | 16 |
| α-helix | 390 | 1 | |
| α-helix | 392-398 | 7 | |
6 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 | 1536 | Saccharomyces cerevisiae | P22579 (AlphaFold model) |
| Transcriptional regulatory protein RCO1 | E, F | protein | 684 | Saccharomyces cerevisiae | Q04779 (AlphaFold model) |
| Histone deacetylase RPD3 | B | protein | 433 | Saccharomyces cerevisiae | P32561 (AlphaFold model) |
| Chromatin modification-related protein EAF3 | C, D, G | protein | 401 | Saccharomyces cerevisiae | Q12432 (AlphaFold model) |
| Histone H3.1 | a, e | protein | 136 | Homo sapiens | P68431 |
| Histone H4 | b, f | protein | 103 | Homo sapiens | P62805 |
| Histone H2A type 1-B/E | c, g | protein | 130 | Homo sapiens | P04908 |
| Histone H2B type 1-K | d, h | protein | 126 | Homo sapiens | O60814 |
| 5-DNA | i | DNA | 147 | Homo sapiens | |
| 3-DNA | j | DNA | 147 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>8W9E_1 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 2 (E, F), FASTA
>8W9E_2 Transcriptional regulatory protein RCO1 (chains E, F)
MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIE
RSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPS
EKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESN
IRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGD
WHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKET
FPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKC
NQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKIT
QIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIY
FQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKK
IIESKPKEELLKFLNIENPENQSE
Sequence of entity 3 (B), FASTA
>8W9E_3 Histone deacetylase RPD3 (chains B)
MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKK
MEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYC
SISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRV
LYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKS
FGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNM
FNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQY
ARDLHVEHDNEFY
Sequence of entity 4 (C, D, G), FASTA
>8W9E_4 Chromatin modification-related protein EAF3 (chains C, D, G)
MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQK
LGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKK
SLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSL
HPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYR
LERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTE
DFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM
Sequence of entity 5 (a, e), FASTA
>8W9E_5 Histone H3.1 (chains a, e)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 6 (b, f), FASTA
>8W9E_6 Histone H4 (chains b, f)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (c, g), FASTA
>8W9E_7 Histone H2A type 1-B/E (chains c, g)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 8 (d, h), FASTA
>8W9E_8 Histone H2B type 1-K (chains d, h)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 9 (i), FASTA
>8W9E_9 5-DNA (chains i)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT
Sequence of entity 10 (j), FASTA
>8W9E_10 3-DNA (chains j)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 7 |
Water and common crystallization additives (K) are not listed.
Primary citation
Structures and dynamics of Rpd3S complex bound to nucleosome. Wang, C., Chu, C., Guo, Z. et al. Sci Adv (2024) 10:eadk7678-eadk7678. DOI 10.1126/sciadv.adk7678 · 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
Browse structure collections
About this viewer
MolViewer shows 8W9E directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.