Rpd3S bound to an H3K36Cme3 modified nucleosome

Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex.

Chromatin modification-related protein EAF3

MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHIL
GYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKS
YNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPD
IYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGR
GTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDA
KKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQ
QVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAY
QDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEID
LDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWF
KNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRK
NQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEII
DALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQT
NKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNV
SESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNL
VEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVG
EDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSA
KDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFL
ERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISK
FLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNI
ETTGNTESSDKGAKIQ

MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTD
EYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGF
CYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD
GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVAR
TWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAED
LGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY

MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEIINGKCFFIH
YQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQ
SFLTSSVSGRKSGRSSANSLHPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT
KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPL
VPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALG
M

MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIERSFKNEHSNLAVEDNIPEEE
PKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPSEKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQ
DLNRNDLKTFLTENMTEESNIRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS
NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLK
KIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDS
YNPDTHIDSNSGKFLICYKCNQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH
CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKITQIDENSIKYDFFDKIYKSKM
VQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIYFQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELD
SIQFNDFSSDEIKHLLYLKKIIESKPKEELLKFLNIENPENQSE

(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG)(DG)(DG)
(DT)(DG)(DG)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DT)(DC)(DG)(DT)(DT)(DG)(DT)(DT)
(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG)(DT)(DC)(DT)(DC)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DG)
(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)
(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)
(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)
(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)
(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)
(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT)(DA)(DT)(DC)(DG)
(DC)(DG)(DC)(DG)(DT)(DG)(DA)(DT)(DC)(DT)(DT)(DA)(DC)(DG)(DG)(DC)(DA)(DT)(DT)(DA)
(DT)(DA)(DC)(DG)(DT)(DA)

TTGTGTTTGGTGTGTCTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCAGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCG
GCACCGGGATTCTGATATCGCGCGTGATCTTACGGCATTATACGTA

(DT)(DA)(DC)(DG)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DC)(DC)(DG)(DT)(DA)(DA)(DG)(DA)(DT)
(DC)(DA)(DC)(DG)(DC)(DG)(DC)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC)
(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)
(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)
(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)
(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)
(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)
(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DG)(DA)(DC)(DA)
(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DC)(DA)(DA)(DC)(DG)(DA)(DA)(DA)(DA)(DC)(DG)(DG)
(DC)(DC)(DA)(DC)(DC)(DA)(DC)(DC)(DC)(DA)(DG)(DA)(DC)(DA)(DC)(DA)(DC)(DC)(DA)(DA)
(DA)(DC)(DA)(DC)(DA)(DA)(DG)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT)

TACGTATAATGCCGTAAGATCACGCGCGATATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGC
ACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCTGGCACGAGACA
GAAAAAAACAACGAAAACGGCCACCACCCAGACACACCAAACACAAGACAGTGAT

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGV(ML3)KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIA
QDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK
TDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII
PRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAH
YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W
RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Richard and Susan Smith Family Foundation
nucleosome, methylation, acetylation, Rpd3S, TRANSCRIPTION, TRANSCRIPTION-DNA complex

AKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY
NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK