2024-11-06 REL RCSB RCSB RCSB 2023-08-03 2024-01-17 2024-01-17 2024-11-06 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) DP2-GM146254 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) DP2-ES036404 United States Richard and Susan Smith Family Foundation United States Rita Allen Foundation United States Damon Runyon Cancer Research Foundation United States Markert JW Vos SM Farnung L nucleosome, methylation, acetylation, Rpd3S, TRANSCRIPTION, TRANSCRIPTION-DNA complex Markert JW Vos SM Farnung L Nat Commun UK 14 8128 8128 2023 38065958 doi:10.1038/s41467-023-43968-8 2041-1723 8tof FULLOVERLAP Rpd3S bound to H3K36Cme3 nucleosome Rpd3S bound to H3K36Cme3 nucleosome 0 1 2 3 4 5 6 7 8 9 10 11 12 Transcriptional regulatory protein SIN3 Saccharomyces cerevisiae 0.175047266 1 Trichoplusia ni LEVO MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHIL GYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKS YNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPD IYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGR GTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDA KKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQ QVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAY QDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEID LDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWF KNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRK NQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEII DALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQT NKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNV SESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNL VEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVG EDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSA KDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFL ERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISK FLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNI ETTGNTESSDKGAKIQ P22579 Histone deacetylase RPD3 Saccharomyces cerevisiae 0.048961957 1 Trichoplusia ni LEVO MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTD EYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGF CYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVAR TWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAED LGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY P32561 3.5.1.98 Chromatin modification-related protein EAF3 Saccharomyces cerevisiae 0.045266406 2 Trichoplusia ni LEVO MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEIINGKCFFIH YQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQ SFLTSSVSGRKSGRSSANSLHPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPL VPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALG M Q12432 Transcriptional regulatory protein RCO1 Saccharomyces cerevisiae 0.07895130499999999 2 Trichoplusia ni LEVO MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIERSFKNEHSNLAVEDNIPEEE PKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPSEKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQ DLNRNDLKTFLTENMTEESNIRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLK KIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDS YNPDTHIDSNSGKFLICYKCNQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKITQIDENSIKYDFFDKIYKSKM VQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIYFQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELD SIQFNDFSSDEIKHLLYLKKIIESKPKEELLKFLNIENPENQSE Q04779 Rco1 Saccharomyces cerevisiae 0.0005156280000000001 1 Trichoplusia ni LEVO (UNK)(UNK)R(UNK)(UNK) DNA (176-MER) synthetic construct 0.06393159 1 (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) DNA DNA (176-MER) synthetic construct 0.066097227 1 (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) DNA Histone H3 Xenopus laevis 0.015495246999999998 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGV(ML3)KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIA QDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA A0A310TTQ1 Histone H4 Xenopus laevis 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG A0A8J1LTD2 Histone H2A Xenopus laevis 0.014109436 2 Escherichia coli LEVO MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B 1.1 Xenopus laevis 0.013655948 2 Escherichia coli LEVO MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAH YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 histone N-terminal tail Xenopus laevis 0.0006578239999999999 1 Escherichia coli LEVO (UNK)(UNK)(UNK)K(UNK)(UNK)(UNK) ZINC ION 6.5409e-05 5 ZN singleParticle particle 7.4 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.25 GATAN K3 BIOQUANTUM (6k x 4k) 51.1 1 2.8 FSC 0.143 CUT-OFF 484141 RANDOM ASSIGNMENT ANGULAR RECONSTITUTION emd_41449_msk_1.map emd_41449_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 369.90002 369.90002 369.90002 90.0 90.0 90.0 X Y Z -0.37381834 0.47088054 0.00040033736 0.035261035 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-41449:::: emd_41449_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 369.90002 369.90002 369.90002 90.0 90.0 90.0 X Y Z 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