+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35081 | |||||||||
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Title | Cryo-EM structure of the histone deacetylase complex Rpd3S | |||||||||
Map data | EM map from 3D refinement | |||||||||
Sample |
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Keywords | Histone deacetylase complex / GENE REGULATION | |||||||||
Function / homology | Function and homology information Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / nucleophagy ...Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / histone deacetylase / cellular response to nitrogen starvation / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / meiotic cell cycle / nuclear periphery / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / heterochromatin formation / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / cellular response to heat / transcription coactivator activity / response to oxidative stress / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Cui H / Wang H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of histone deacetylase complex Rpd3S bound to nucleosome. Authors: Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang / Abstract: Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is ...Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35081.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-35081-v30.xml emd-35081.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35081_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_35081.png | 137.1 KB | ||
Filedesc metadata | emd-35081.cif.gz | 8.1 KB | ||
Others | emd_35081_half_map_1.map.gz emd_35081_half_map_2.map.gz | 49.9 MB 49.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35081 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35081 | HTTPS FTP |
-Related structure data
Related structure data | 8hxxMC 8hxyC 8hxzC 8hy0C 8jhoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35081.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM map from 3D refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: EM half-map 2
File | emd_35081_half_map_1.map | ||||||||||||
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Annotation | EM half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half-map 1
File | emd_35081_half_map_2.map | ||||||||||||
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Annotation | EM half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rpd3S histone deacetylase in complex with histone H3 tail
Entire | Name: Rpd3S histone deacetylase in complex with histone H3 tail |
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Components |
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-Supramolecule #1: Rpd3S histone deacetylase in complex with histone H3 tail
Supramolecule | Name: Rpd3S histone deacetylase in complex with histone H3 tail type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Transcriptional regulatory protein SIN3
Macromolecule | Name: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 175.047266 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE ...String: MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE KATQRPQDCK EVPAGVQPAD APDPSSNHAD ANDDNNNNEN SHDEDADYRP LNVKDALSYL EQVKFQFSSR PD IYNLFLD IMKDFKSQAI DTPGVIERVS TLFRGYPILI QGFNTFLPQG YRIECSSNPD DPIRVTTPMG TTTVNNNISP SGR GTTDAQ ELGSFPESDG NGVQQPSNVP MVPSSVYQSE QNQDQQQSLP LLATSSGLPS IQQPEMPAHR QIPQSQSLVP QEDA KKNVD VEFSQAISYV NKIKTRFADQ PDIYKHFLEI LQTYQREQKP INEVYAQVTH LFQNAPDLLE DFKKFLPDSS ASANQ QVQH AQQHAQQQHE AQMHAQAQAQ AQAQAQVEQQ KQQQQFLYPA SGYYGHPSNR GIPQQNLPPI GSFSPPTNGS TVHEAY QDQ QHMQPPHFMP LPSIVQHGPN MVHQGIANEN PPLSDLRTSL TEQYAPSSIQ HQQQHPQSIS PIANTQYGDI PVRPEID LD PSIVPVVPEP TEPIENNISL NEEVTFFEKA KRYIGNKHLY TEFLKILNLY SQDILDLDDL VEKVDFYLGS NKELFTWF K NFVGYQEKTK CIENIVHEKH RLDLDLCEAF GPSYKRLPKS DTFMPCSGRD DMCWEVLNDE WVGHPVWASE DSGFIAHRK NQYEETLFKI EEERHEYDFY IESNLRTIQC LETIVNKIEN MTENEKANFK LPPGLGHTSM TIYKKVIRKV YDKERGFEII DALHEHPAV TAPVVLKRLK QKDEEWRRAQ REWNKVWREL EQKVFFKSLD HLGLTFKQAD KKLLTTKQLI SEISSIKVDQ T NKKIHWLT PKPKSQLDFD FPDKNIFYDI LCLADTFITH TTAYSNPDKE RLKDLLKYFI SLFFSISFEK IEESLYSHKQ NV SESSGSD DGSSIASRKR PYQQEMSLLD ILHRSRYQKL KRSNDEDGKV PQLSEPPEEE PNTIEEEELI DEEAKNPWLT GNL VEEANS QGIIQNRSIF NLFANTNIYI FFRHWTTIYE RLLEIKQMNE RVTKEINTRS TVTFAKDLDL LSSQLSEMGL DFVG EDAYK QVLRLSRRLI NGDLEHQWFE ESLRQAYNNK AFKLYTIDKV TQSLVKHAHT LMTDAKTAEI MALFVKDRNA STTSA KDQI IYRLQVRSHM SNTENMFRIE FDKRTLHVSI QYIALDDLTL KEPKADEDKW KYYVTSYALP HPTEGIPHEK LKIPFL ERL IEFGQDIDGT EVDEEFSPEG ISVSTLKIKI QPITYQLHIE NGSYDVFTRK ATNKYPTIAN DNTQKGMVSQ KKELISK FL DCAVGLRNNL DEAQKLSMQK KWENLKDSIA KTSAGNQGIE SETEKGKITK QEQSDNLDSS TASVLPASIT TVPQDDNI E TTGNTESSDK GAKIQ UniProtKB: Transcriptional regulatory protein SIN3 |
-Macromolecule #2: Histone deacetylase RPD3
Macromolecule | Name: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 48.961957 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL ...String: MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL GIIELLRYHP RVLYIDIDVH HGDGVEEAFY TTDRVMTCSF HKYGEFFPGT GELRDIGVGA GKNYAVNVPL RD GIDDATY RSVFEPVIKK IMEWYQPSAV VLQCGGDSLS GDRLGCFNLS MEGHANCVNY VKSFGIPMMV VGGGGYTMRN VAR TWCFET GLLNNVVLDK DLPYNEYYEY YGPDYKLSVR PSNMFNVNTP EYLDKVMTNI FANLENTKYA PSVQLNHTPR DAED LGDVE EDSAEAKDTK GGSQYARDLH VEHDNEFY UniProtKB: Histone deacetylase RPD3 |
-Macromolecule #3: Chromatin modification-related protein EAF3
Macromolecule | Name: Chromatin modification-related protein EAF3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 45.266406 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS ...String: MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS GRKSGRSSAN SLHPGSSLRS SSDQNGNDDR RRSSSLSPNM LHHIAGYPTP KISLQIPIKL KSVLVDDWEY VT KDKKICR LPADVTVEMV LNKYEHEVSQ ELESPGSQSQ LSEYCAGLKL YFDKCLGNML LYRLERLQYD ELLKKSSKDQ KPL VPIRIY GAIHLLRLIS VLPELISSTT MDLQSCQLLI KQTEDFLVWL LMHVDEYFND KDPNRSDDAL YVNTSSQYEG VALG M UniProtKB: Chromatin modification-related protein EAF3 |
-Macromolecule #4: RCO1 isoform 1
Macromolecule | Name: RCO1 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 78.951305 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK ...String: MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK TFLTENMTEE SNIRSTIGWN GDIINRTRDR EPESDRDNKK LSNIRTKIIL STNATYDSKS KLFGQNSIKS TS NASEKIF RDKNNSTIDF ENEDFCSACN QSGSFLCCDT CPKSFHFLCL DPPIDPNNLP KGDWHCNECK FKIFINNSMA TLK KIESNF IKQNNNVKIF AKLLFNIDSH NPKQFQLPNY IKETFPAVKT GSRGQYSDEN DKIPLTDRQL FNTSYGQSIT KLDS YNPDT HIDSNSGKFL ICYKCNQTRL GSWSHPENSR LIMTCDYCQT PWHLDCVPRA SFKNLGSKWK CPLHSPTKVY KKIHH CQED NSVNYKVWKK QRLINKKNQL YYEPLQKIGY QNNGNIQIIP TTSHTDYDFN QDFKITQIDE NSIKYDFFDK IYKSKM VQK RKLFQFQESL IDKLVSNGSQ NGNSEDNMVK DIASLIYFQV SNNDKSSNNK SASKSNNLRK LWDLKELTNV VVPNELD SI QFNDFSSDEI KHLLYLKKII ESKPKEELLK FLNIENPENQ SE UniProtKB: RCO1 isoform 1 |
-Macromolecule #5: Histone H3
Macromolecule | Name: Histone H3 / type: protein_or_peptide / ID: 5 Details: Author stated that Cys110 residue of chain E was mutated to Ala due to the preparation of ML3-modified nucleosome. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 15.331982 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(ML3)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3 |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8hxx: |