+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11101 | |||||||||
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Title | HDAC-TC | |||||||||
Map data | HDAC-TC | |||||||||
Sample |
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Keywords | Protein complex / GENE REGULATION | |||||||||
Function / homology | Function and homology information HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / epigenetic regulation of gene expression ...HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase activity / histone deacetylase complex / epigenetic regulation of gene expression / chromosome segregation / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Lee J-H / Bollschweiler D | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies. Authors: Jung-Hoon Lee / Daniel Bollschweiler / Tillman Schäfer / Robert Huber / Abstract: The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup ...The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11101.map.gz | 763.4 MB | EMDB map data format | |
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Header (meta data) | emd-11101-v30.xml emd-11101.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_11101.png | 29.5 KB | ||
Filedesc metadata | emd-11101.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11101 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11101 | HTTPS FTP |
-Validation report
Summary document | emd_11101_validation.pdf.gz | 674.6 KB | Display | EMDB validaton report |
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Full document | emd_11101_full_validation.pdf.gz | 674.1 KB | Display | |
Data in XML | emd_11101_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | emd_11101_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11101 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11101 | HTTPS FTP |
-Related structure data
Related structure data | 6z6oMC 6z6fC 6z6hC 6z6pC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11101.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HDAC-TC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HDAC-TC
Entire | Name: HDAC-TC |
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Components |
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-Supramolecule #1: HDAC-TC
Supramolecule | Name: HDAC-TC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
-Macromolecule #1: Histone deacetylase HDA1
Macromolecule | Name: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: histone deacetylase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Molecular weight | Theoretical: 74.851953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RQVIVPVCMP KIHYSPLKTG LCYDVRMRYH AKIFTSYFEY IDPHPEDPRR IYRIYKILAE NGLINDPTLS GVDDLGDLML KIPVRAATS EEILEVHTKE HLEFIESTEK MSREELLKET EKGDSVYFNN DSYASARLPC GGAIEACKAV VEGRVKNSLA V VRPPGHHA ...String: RQVIVPVCMP KIHYSPLKTG LCYDVRMRYH AKIFTSYFEY IDPHPEDPRR IYRIYKILAE NGLINDPTLS GVDDLGDLML KIPVRAATS EEILEVHTKE HLEFIESTEK MSREELLKET EKGDSVYFNN DSYASARLPC GGAIEACKAV VEGRVKNSLA V VRPPGHHA EPQAAGGFCL FSNVAVAAKN ILKNYPESVR RIMILDWDIH HGNGTQKSFY QDDQVLYVSL HRFEMGKYYP GT IQGQYDQ TGEGKGEGFN CNITWPVGGV GDAEYMWAFE QVVMPMGREF KPDLVIISSG FDAADGDTIG QCHVTPSCYG HMT HMLKSL ARGNLCVVLE GGYNLDAIAR SALSVAKVLI GEPPDELPDP LSDPKPEVIE MIDKVIRLQS KYWNCFRRRH ANSG CNFNE PLNDSIISKN FPLQKAIRQQ QQHYLSDEFN FVTLPLVSMD LPDNTVLCTP NISESNTIII VVHDTSDIWA KRNVI SGTI DLSSSVIIDN SLDFIKWGLD RKYGIIDVNI PLTLFEPDNY SGMITSQEVL IYLWDNYIKY FPSVAKIAFI GIGDSY SGI VHLLGHRDTR AVTKTVINFL GDKQLKPLVP LVDETLSEWY FKNSLIFSNN SHQCWKENES RKPRKKFGRV LRCDTDG LN NIIEERFEEA TDFILDSFE UniProtKB: Histone deacetylase HDA1 |
-Macromolecule #2: Histone deacetylase HDA1
Macromolecule | Name: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: histone deacetylase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Molecular weight | Theoretical: 76.017211 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ENSLSTTSKS KRQVIVPVCM PKIHYSPLKT GLCYDVRMRY HAKIFTSYFE YIDPHPEDPR RIYRIYKILA ENGLINDPTL SGVDDLGDL MLKIPVRAAT SEEILEVHTK EHLEFIESTE KMSREELLKE TEKGDSVYFN NDSYASARLP CGGAIEACKA V VEGRVKNS ...String: ENSLSTTSKS KRQVIVPVCM PKIHYSPLKT GLCYDVRMRY HAKIFTSYFE YIDPHPEDPR RIYRIYKILA ENGLINDPTL SGVDDLGDL MLKIPVRAAT SEEILEVHTK EHLEFIESTE KMSREELLKE TEKGDSVYFN NDSYASARLP CGGAIEACKA V VEGRVKNS LAVVRPPGHH AEPQAAGGFC LFSNVAVAAK NILKNYPESV RRIMILDWDI HHGNGTQKSF YQDDQVLYVS LH RFEMGKY YPGTIQGQYD QTGEGKGEGF NCNITWPVGG VGDAEYMWAF EQVVMPMGRE FKPDLVIISS GFDAADGDTI GQC HVTPSC YGHMTHMLKS LARGNLCVVL EGGYNLDAIA RSALSVAKVL IGEPPDELPD PLSDPKPEVI EMIDKVIRLQ SKYW NCFRR RHANSGCNFN EPINDSIISK NFPLQKAIRQ QQQHYLSDEF NFVTLPLVSM DLPDNTVLCT PNISESNTII IVVHD TSDI WAKRNVISGT IDLSSSVIID NSLDFIKWGL DRKYGIIDVN IPLTLFEPDN YSGMITSQEV LIYLWDNYIK YFPSVA KIA FIGIGDSYSG IVHLLGHRDT RAVTKTVINF LGDKQLKPLV PLVDETLSEW YFKNSLIFSN NSHQCWKENE SRKPRKK FG RVLRCDTDGL NNIIEERFEE ATDFILDSFE UniProtKB: Histone deacetylase HDA1 |
-Macromolecule #3: HDA1 complex subunit 2
Macromolecule | Name: HDA1 complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Molecular weight | Theoretical: 71.915297 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KVYYLPVTLT QFQKDLSEIL ISLHAKSFKA SIIGEPQADA VNKPSGLPAG PETHPYPTLS QRQLTYIFDS NIRAIANHPS LLVDHYMPR QLLRMEPTES SIAGSHKFQV LNQLINSICF RDREGSPNEV IKCAIIAHSI KELDLLEGLI LGKKFRTKRL S GTSLYNEK ...String: KVYYLPVTLT QFQKDLSEIL ISLHAKSFKA SIIGEPQADA VNKPSGLPAG PETHPYPTLS QRQLTYIFDS NIRAIANHPS LLVDHYMPR QLLRMEPTES SIAGSHKFQV LNQLINSICF RDREGSPNEV IKCAIIAHSI KELDLLEGLI LGKKFRTKRL S GTSLYNEK HKFPNLPTVD STINKDGTPN SVSSTSSNSN STSYTGYSKD DYDYSVKRNL KKRKINTDDW LFLATTKHLK HD QYLLANY DIDMIISFDP MLEVELPALQ VLRNNANKDI PIIKLLVQNS PDHYLLDSEI KNSSVKSSHL SNNGHVDDSQ EYE EIKSSL LYFLQARNAP VNNCEIDYIK LVKCCLEGKD CNNILPVLDL ITLDEASKDS SDSGFWQPQL TKLQYSSTEL PLWD GPLDI KTYQTELMHR AVIRLRDIQD EYAKGTVPLY EKRLNETQRQ NQLDEIKNSV GLTFKKKQEV EKSINDSEKR LKHAM TEST KLQNKINHLL KNRQELENFN KLPSNTISSE NHLEEGSALA DKLKEYIDKN ATLFNKLKEL QQANAEKSKL NDELRS KYQ IESSKAAESA QTLKILQESM KSLENEVNGP LTKFSTESLK KELERLQNDF QSLKARNKFL KNYITL UniProtKB: HDA1 complex subunit 2 |
-Macromolecule #4: HDA1 complex subunit 3,HDA1 complex subunit 3
Macromolecule | Name: HDA1 complex subunit 3,HDA1 complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Molecular weight | Theoretical: 63.292918 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGDYWLPTTM SLYQKELTDQ IVSLHYSDIL RYFETSHYKE DVILESMKTM CLNGSLVATH PYLLIDHYMP KSLITRDVPA HLAENSGKF SVLRDLINLV QEYETETAIV CRPGRTMDLL EALLLGNKVH IKRYDGHSIK SKQKANDFSC TVHLFSSEGI N FTKYPIKS ...String: SGDYWLPTTM SLYQKELTDQ IVSLHYSDIL RYFETSHYKE DVILESMKTM CLNGSLVATH PYLLIDHYMP KSLITRDVPA HLAENSGKF SVLRDLINLV QEYETETAIV CRPGRTMDLL EALLLGNKVH IKRYDGHSIK SKQKANDFSC TVHLFSSEGI N FTKYPIKS KARFDMLICL DTTVDTSQKD IQYLLQYKRE RKGLERYAPI VRLVAINSID HCRLFFGKKF DKNSREYLEN VT AAMVILR DRLGTLPPDL RPIYSQKLHY LVEWLENPTV PWPLPDIYPL KQYTSMDVER SLLTEVHFKN SSNVNYHLSS GII THKLIQ SMGEVYMDIC VQKQELDDYS CLDDLQNDHL KFFSNEDEKI IKEYETVLRT NNENLNRSHE LEVENNLKFS QIET LEKDI ETLKGSLMAQ GETLSKLKDA FVKTDNVQDE IEKEERVSVS RDTEKKYMEQ EIKRAVDAIR ENEEETHKLN EKQNG LESE LKLKFEKSEI STKELNEKIG FLKKELKLEN DLNEELVGQL SKTMDNLENL TIPRVRTQ UniProtKB: HDA1 complex subunit 3, HDA1 complex subunit 3 |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 8 / 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 86.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 53757 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Details | Real space refinement |
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Output model | PDB-6z6o: |