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Yorodumi- EMDB-11041: The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetyla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11041 | ||||||||||||
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Title | The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex | ||||||||||||
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Sample |
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Keywords | HDAC1 MIDEAS ELMSAN1 DNTTIP1 TDIF1 histone deacetylase MiDAC / GENE REGULATION | ||||||||||||
Function / homology | Function and homology information Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / regulation of cell fate specification ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / protein deacetylation / Transcription of E2F targets under negative control by DREAM complex / STAT3 nuclear events downstream of ALK signaling / histone deacetylase / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / negative regulation of gene expression, epigenetic / positive regulation of oligodendrocyte differentiation / histone deacetylase activity / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / eyelid development in camera-type eye / oligodendrocyte differentiation / E-box binding / odontogenesis of dentin-containing tooth / RNA Polymerase I Transcription Initiation / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / G0 and Early G1 / NF-kappaB binding / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / nucleosome binding / Regulation of TP53 Activity through Acetylation / transcription repressor complex / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / hippocampus development / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of smooth muscle cell proliferation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / neuron differentiation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / transcription corepressor activity / p53 binding / chromatin organization / chromosome / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / neuronal cell body / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Fairall L / Saleh A | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nucleic Acids Res / Year: 2015 Title: Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting. Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino ...Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino / John W R Schwabe / Abstract: Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and ...Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex. | ||||||||||||
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_11041.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-11041-v30.xml emd-11041.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
Images | emd_11041.png | 38.3 KB | ||
Masks | emd_11041_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-11041.cif.gz | 7.5 KB | ||
Others | emd_11041_half_map_1.map.gz emd_11041_half_map_2.map.gz | 192.5 MB 192.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11041 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11041 | HTTPS FTP |
-Validation report
Summary document | emd_11041_validation.pdf.gz | 335.9 KB | Display | EMDB validaton report |
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Full document | emd_11041_full_validation.pdf.gz | 335 KB | Display | |
Data in XML | emd_11041_validation.xml.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11041 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11041 | HTTPS FTP |
-Related structure data
Related structure data | 6z2jMC 6z2kC 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_11041.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11041_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11041_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11041_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric complex of the MiDAC deacetylase complex containing HDAC1...
Entire | Name: Dimeric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1 |
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Components |
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-Supramolecule #1: Dimeric complex of the MiDAC deacetylase complex containing HDAC1...
Supramolecule | Name: Dimeric complex of the MiDAC deacetylase complex containing HDAC1, the ELM2-SANT domain of MIDEAS and the dimerisation domain of DNTTIP1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 178 KDa |
-Macromolecule #1: Histone deacetylase 1
Macromolecule | Name: Histone deacetylase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.178906 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ ...String: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ RVLYIDIDIH HGDGVEEAFY TTDRVMTVSF HKYGEYFPGT GDLRDIGAGK GKYYAVNYPL RDGIDDESYE AI FKPVMSK VMEMFQPSAV VLQCGSDSLS GDRLGCFNLT IKGHAKCVEF VKSFNLPMLM LGGGGYTIRN VARCWTYETA VAL DTEIPN ELPYNDYFEY FGPDFKLHIS PSNMTNQNTN EYLEKIKQRL FENLRMLPHA PGVQMQAIPE DAIPEESGDE DEDD PDKRI SICSSDKRIA CEEEFSDSEE EGEGGRKNSS NFKKAKRVKT EDEKEKDPEE KKEVTEEEKT KEEKPEAKGV KEEVK LA UniProtKB: Histone deacetylase 1 |
-Macromolecule #2: Deoxynucleotidyltransferase terminal-interacting protein 1
Macromolecule | Name: Deoxynucleotidyltransferase terminal-interacting protein 1 type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.381293 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGATGDAEQP RGPSGAERGG LELGDAGAAG QLVLTNPWNI MIKHRQVQRR GRRSQMTTSF TDPAISMDLL RAVLQPSINE EIQTVFNKY MKFFQKAALN VRDNVGEEVD AEQLIQEACR SCLEQAKLLF S UniProtKB: Deoxynucleotidyltransferase terminal-interacting protein 1 |
-Macromolecule #3: Mitotic deacetylase-associated SANT domain protein
Macromolecule | Name: Mitotic deacetylase-associated SANT domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 19.794771 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GAVSIEPRIN VGSRFQAEIP LMRDRALAAA DPHKADLVWQ PWEDLESSRE KQRQVEDLLT AACSSIFPGA GTNQELALHC LHESRGDIL ETLNKLLLKK PLRPHNHPLA TYHYTGSDQW KMAERKLFNK GIAIYKKDFF LVQKLIQTKT VAQCVEFYYT Y KKQVKIGR NGTLT UniProtKB: Mitotic deacetylase-associated SANT domain protein |
-Macromolecule #4: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 sec at 30 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 3 sec, blot force 10.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 2752 / Average exposure time: 60.0 sec. / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 129629 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |