PDBi (Protein Data Bank in India)

All in One Protein Databank
Home About Help Resources External Links Contact Us
Advanced Search
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

9V2V

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

PDB DOI: 10.2210/pdb9v2v/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: 3.0 Å

9v2v
Literature

Cryo-em structure of the histone deacetylase complex rpd3l in complex with mono-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: 9V2V


Proteins
Molecule Chains Sequence Length Organism Sequence
Transcriptional regulatory protein SIN3 A 683 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALP
Transcriptional regulatory protein SIN3 B 683 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALP
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 H2B P 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Histone H2B T 93 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
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 H4 R 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone H4 V 79 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
Histone deacetylase RPD3 C 385 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNH
Histone deacetylase RPD3 D 385 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNH
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 121 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis RLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQ
Transcriptional regulatory protein RXT3 H 211 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILVLRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYPSVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQ
Transcriptional regulatory protein PHO23 I 105 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT
Transcriptional regulatory protein RXT2 J 218 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis SKLVNVKEILTPILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYL
Histone deacetylase complex subunit CTI6 K 249 Saccharomyces Cerevisiae S288C , Synthetic Construct , Xenopus Laevis TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLTEGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTSISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQRTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLSMMDDLTREL

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
DNA (155-MER) x 155 NA TCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGG
DNA (155-MER) y 155 NA CCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCTAGA
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.