Cryo-EM structure of a SIN3/HDAC complex from budding yeast

2025-07-23 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID STRUCTURE_SUMMARY atom_site chem_comp_atom chem_comp_bond em_admin em_entity_assembly em_software entity entity_poly entity_poly_seq entity_src_nat pdbx_entity_nonpoly pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly_gen pdbx_struct_conn_angle pdbx_struct_mod_residue pdbx_unobs_or_zero_occ_residues pdbx_validate_close_contact struct_asym struct_conn struct_ref_seq _em_admin.last_update _em_entity_assembly.entity_id_list _em_software.name _entity_poly.pdbx_seq_one_letter_code _entity_poly_seq.mon_id _entity_src_nat.common_name _pdbx_entry_details.has_protein_modification _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_validate_close_contact.auth_seq_id_2 _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq.pdbx_auth_seq_align_end STRUCTURE_SUMMARY em_admin em_entity_assembly em_software entity entity_poly entity_src_nat struct_ref_seq _em_admin.last_update _em_entity_assembly.entity_id_list _em_software.name _entity_poly.pdbx_seq_one_letter_code _entity_src_nat.common_name _struct_ref_seq.pdbx_auth_seq_align_end PDBj PDBc 2022-12-12 2023-05-03 2023-05-03 2025-07-23 National Natural Science Foundation of China (NSFC) China Cryo-EM structure of a SIN3/HDAC complex from budding yeast Guo Z Zhan X Wang C SIN3, HDAC, deacetylase, Rpd3, DNA BINDING PROTEIN Guo Z Chu C Lu Y Zhang X Xiao Y Wu M Gao S Wong CCL Zhan X Wang C Structure of a SIN3-HDAC complex from budding yeast. Nat.Struct.Mol.Biol. US 30 753 760 2023 37081318 doi:10.1038/s41594-023-00975-z 1545-9985 8hpo FULLOVERLAP The Rpd3L complex The Rpd3L complex 0 1 2 4 5 6 7 8 9 10 Saccharomyces cerevisiae Transcriptional regulatory protein UME1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.051075602 1 LEVO MSTLDIAEDNKIKNEEFKIWKKSIPSLYQHISSLKPIFGSGVDESPSTLRSIVFTNDSSCNKSKGVLSVPLLYSQGSEIF EVDCIVPLGLHYKKPESISEPLVQPDYTMESQKVEQTVLIPKWEFKGETIAKMIYVDNSEINVKVIALSTNGSLAWFREG VKSPVYTMMEPSTSLSSASSGNQNKPCVDFAISNDSKTLTVTKEKHLDNENATIKLIDNSGKIGEVLRTIPVPGIKNIQE IKFLNNQIFATCSDDGIIRFWGNEIGKKPLWILNDSLDGKTTCFAASPFVDTLFMTGTSGGALKVWDIRAVIALGDADAE LNINQGHNKVNELFKVHHFYSEQVSKIEFSSISPMEVVTIGGLGNVYHWNFEPVFAIYNEIHEDFQGIISDELEAESMAF YHTEGCRREIGENNKVNTVAYHKYIEDLVATVDSDGLLTVYKPFTGKVLDGSREVGAAKS Q03010 Transcriptional regulatory protein SDS3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.037765277 1 LEVO MAIQKVSNKDLSRKDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRL RLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHT VSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTY KSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDI(SEP)LIRELTG QPPAPFRLRSD P40505 Histone deacetylase RPD3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.049441828 1 LEVO MVYEA(TPO)PFDPI(TPO)VKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQ EMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHA KKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNY AVNVPLRDGIDDATYRSVFEPVIKKIMEWYQP(SEP)AVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVV GGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVN(TPO)PEYLDKVMTNIFANLENTK YAP(SEP)VQLNH(TPO)PRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY P32561 3.5.1.98 Histone deacetylase RPD3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.048961957 1 LEVO MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTD EYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGF CYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRD GIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVAR TWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAED LGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY P32561 3.5.1.98 Transcriptional regulatory protein SAP30 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.023144192999999997 1 LEVO MARPVNTNAETESRGRPTQGGGYASNNNGSCNNNNGSNNNNNNNNNNNNNSNNSNNNNGPTSSGRTNGKQRLTAAQQQYI KNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKR DLANVVRRHFDEH(SEP)IKETDCIPQFIYKVKNQKKKFKMEFRG P38429 Transcriptional regulatory protein SIN3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.175047266 2 LEVO MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHIL GYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKS YNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPD IYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGR GTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDA KKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQ QVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAY QDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEID LDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWF KNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRK NQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEII DALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQT NKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNV SESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNL VEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVG EDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSA KDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFL ERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISK FLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNI ETTGNTESSDKGAKIQ P22579 Transcriptional regulatory protein DEP1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.047035722999999995 1 LEVO MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEKSLANLPELKYAPKLSSLVKQ ETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENE HTAPPALVMPSPIEMEEQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHR AYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVIPDVNYHVPIKLDNKTLSCIT GYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIVDRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDF HQWAQ P31385 Transcriptional regulatory protein PHO23 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.03708143 1 LEVO MSSPANLFPGLNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELM PSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNTEIPRGLRLGVDNHPAMHLHHELMEKIESKSNSKSSQALKSESRRE AMAANRRQGEHYSASTHQQDDSKNDANYGGSRHESQDHTGNNTNSRKRANAANTNNADPETKKRKRRVATTAVSPSTIST ATAVNNGRIGTSTASRGVSSVGNSNNSRISRPKTNDYGEPLYCYCNQVAYGEMVGCDGADCELEWFHLPCIGLETLPKGK WYCDDCKKKL P50947 Transcriptional regulatory protein RXT2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.048844043 1 LEVO MTIRSSMKNNAELESKSVLANESNIISTFTRRIIKEKSGNYQVLKRSLDGKLIYPEATGISSNRGNKLLQRSEVVTRRDL NNSKPMIEQTVFYNGSEHRLLQTNIVTDSRRKRIKFTPDINVEPVLVGDENDIDGSEKEDENITDEYYGEEDDDDLSKLV NVKEIL(TPO)PIL(SEP)LGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLN LPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSAS ISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYLGISDDDITIPVALRVVKR GLISATTNKTTNFEEEIENTMEDGVVDDNEPDEEANRA P38255 Transcriptional regulatory protein RXT3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.033851535 1 LEVO MSVSEQDPNRAYRETQSQIYKLQETLLNSARTKNKQEEGQESNTHSFPEQYMHYQNGRNSAYDLPNVSSQSVLAFTEKHY PNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRK RNNEIWGCDIYSDDSDPILVLRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYP SVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQRLDRDKPHEPNGYIKNLKWT Q07458 ZINC ION 6.5409e-05 2 ZN POTASSIUM ION 3.9098e-05 4 K singleParticle particle 7.4 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.8 2.3000000000000003 GATAN K3 (6k x 4k) 50.0 1 NONE 2.6 FSC 0.143 CUT-OFF 665105 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_34935.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 434.80002 434.80002 434.80002 90.0 90.0 90.0 X Y Z -2.6639845 4.4420238 0.00095071626 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