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FASTA Sequence PDB Format mmCIF Format
FASTA Sequence PDB Format PDB Format(gz) PDBx/mmCIF Format PDBx/mmCIF Format(gz) PDBML/XML Format Validation Full PDF Validation CIF

9V2W

Cryo-em structure of the histone deacetylase complex rpd3l in complex with di-nucleosome

PDB DOI: 10.2210/pdb9v2w/pdb

Classification: GENE REGULATION/DNA
Organism(s): Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis

Deposited: 2025-05-21
Deposition Author(s): Chao, W. , Dong, S. , He, J. , Li, H. , Li, H. , Pei, D. , Qin, D. , Wang, C. , Xie, Y. , Yang, X. , Yi, L. , Zhang, N. , Zhang, Y. , Zhao, H. , Zhou, Y. , Zou, B.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.4 Å

9v2w
Literature

Cryo-em structure of the histone deacetylase complex rpd3l in complex with di-nucleosome

Chao, W. , Dong, S. , He, J. , Li, H. , Li, H. , Pei, D. , Qin, D. , Wang, C. , Xie, Y. , Yang, X. , Yi, L. , Zhang, N. , Zhang, Y. , Zhao, H. , Zhou, Y. , Zou, B.

Primary Citation of Related Structures: 9V2W


Proteins
Molecule Chains Sequence Length Organism Sequence
Transcriptional regulatory protein SIN3 A 1096 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALD
Transcriptional regulatory protein RXT2 J 206 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis ILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYL
Histone deacetylase complex subunit CTI6 K 249 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLTEGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTSISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQRTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLSMMDDLTREL
Histone H4 L 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone H4 R 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone H4 V 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone H4 Z 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone H2A B 107 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Histone H2A M 107 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Histone H2A O 107 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Histone H2A S 107 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
Histone deacetylase RPD3 C 378 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYA
Histone H2B D 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Histone H2B N 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Histone H2B P 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Histone H2B T 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Transcriptional regulatory protein DEP1 E 119 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis EQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRD
Transcriptional regulatory protein SDS3 F 311 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRELTGQPPAPFRL
Transcriptional regulatory protein SAP30 G 119 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis TAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQ
Histone H3 H 98 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Histone H3 Q 98 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Histone H3 U 98 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Histone H3 W 98 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Transcriptional regulatory protein PHO23 I 105 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
DNA (329-MER) x 329 NA GACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGAAGACCACCATGGAATTCATGGCGGAAGCATGACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGA
DNA (329-MER) y 329 NA TCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTCATGCTTCCGCCATGAATTCCATGGTGGTCTTCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTC
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2025-05-21
Deposition Author(s): Chao, W. , Dong, S. , He, J. , Li, H. , Li, H. , Pei, D. , Qin, D. , Wang, C. , Xie, Y. , Yang, X. , Yi, L. , Zhang, N. , Zhang, Y. , Zhao, H. , Zhou, Y. , Zou, B.