2025-07-02 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details pdbx_modification_feature _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification PDBj PDBj 2023-08-09 2023-09-13 2023-09-13 2025-07-02 National Natural Science Foundation of China (NSFC) NSFC U20A2013 China National Natural Science Foundation of China (NSFC) 32241021 China National Natural Science Foundation of China (NSFC) 32170189 China Other government MYRG2018-00221-FHS Other government 0009/2018/A1 Other government 0032/2021/A1 Other government 202102080156 Other government 2019QN01Y051 Dong S Li H Meilin W Rasheed N Zou B Gao X Guan J Li W Zhang J Wang C Zhou N Shi X Li M Zhou M Huang J Li H Zhang Y Wong KH Zhang X Chao WCH He J Rpd3S, HDAC, Hho1, cryptic transcription, TRANSCRIPTION Dong S Li H Wang M Rasheed N Zou B Gao X Guan J Li W Zhang J Wang C Zhou N Shi X Li M Zhou M Huang J Li H Zhang Y Wong KH Zhang X Chao WCH He J Cell Res. CN 33 790 801 2023 37666978 doi:10.1038/s41422-023-00869-1 1001-0602 8kd5 FULLOVERLAP H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2 H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2 0 1 2 3 4 5 6 7 8 9 10 Rpd3-Sin3-Eaf3-Rco1 1 1 8 9 10 Saccharomyces cerevisiae Histone 1 2 3 4 5 Xenopus laevis 187bp DNA 1 6 7 synthetic construct Chromatin modification-related protein EAF3 Saccharomyces cerevisiae 0.045266406 2 Trichoplusia ni LEVO MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEIINGKCFFIH YQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQ SFLTSSVSGRKSGRSSANSLHPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVT KDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPL VPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALG M Q12432 Histone H3 Xenopus laevis 0.015313942999999998 2 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGV(M3L)KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA A0A310TTQ1 Histone H4 Xenopus laevis 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.013978240999999999 2 Escherichia coli LEVO SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B 1.1 Xenopus laevis 0.013524752 2 Escherichia coli LEVO AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 187bp DNA synthetic construct 0.058077925999999995 1 (DG)(DC)(DG)(DG)(DT)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(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)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DT)(DC)(DC) DNA 187bp DNA synthetic construct 0.057397496 1 (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(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)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DT)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC)(DC)(DA)(DC)(DC)(DG)(DC) DNA Histone deacetylase RPD3 Saccharomyces cerevisiae 0.048961957 1 Trichoplusia ni LEVO MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTD EYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGF CYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVAR TWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAED LGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY P32561 Transcriptional regulatory protein SIN3 Saccharomyces cerevisiae 0.176152438 1 Trichoplusia ni LEVO MHHHHHHHHSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQAL TSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAP VHTEEPKSYNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVK FQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVN NNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQ SLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLP DSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTN GSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGD IPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGS NKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASED SGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYD KERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEI SSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEES LYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAK NPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLS EMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKD RNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPH EKLKIPFLERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVS QKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASIT TVPQDDNIETTGNTESSDKGAKIQ P22579 Transcriptional regulatory protein RCO1 Saccharomyces cerevisiae 0.07895130499999999 2 Trichoplusia ni LEVO MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIERSFKNEHSNLAVEDNIPEEE PKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPSEKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQ DLNRNDLKTFLTENMTEESNIRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTS NASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLK KIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDS YNPDTHIDSNSGKFLICYKCNQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHH CQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKITQIDENSIKYDFFDKIYKSKM VQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIYFQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELD SIQFNDFSSDEIKHLLYLKKIIESKPKEELLKFLNIENPENQSE Q04779 ZINC ION 6.5409e-05 1 ZN singleParticle threeDArray 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.2 FEI FALCON IV (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.9 FSC 0.143 CUT-OFF 109319 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_37125_msk_1.map emd_37125_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 383.4 383.4 383.4 90.0 90.0 90.0 X Y Z -0.93661654 1.4419543 0.08482781 0.1262799 0.71 0.71 0.71 AUTHOR ::::EMDATABANK.org::::EMD-37125:::: emd_37125_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 383.4 383.4 383.4 90.0 90.0 90.0 X Y Z -0.8124034 1.396971 0.08495027 0.12645526 0.71 0.71 0.71 AUTHOR ::::EMDATABANK.org::::EMD-37125::::