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Yorodumi- PDB-5icn: HDAC1:MTA1 in complex with inositol-6-phosphate and a novel pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5icn | ||||||||||||||||||
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Title | HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4 | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Transcription repression Inositol phosphate Corepressor Histone deacetylase HDAC1 HDAC3 Histones / Metastasis associated protein / IP6 | ||||||||||||||||||
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 / regulation of amyloid-beta clearance / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / regulation of amyloid-beta clearance / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / NuRD complex / regulation of cell fate specification / endoderm development / DNA methylation-dependent heterochromatin formation / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / protein deacetylation / STAT3 nuclear events downstream of ALK signaling / histone deacetylase / positive regulation of protein autoubiquitination / protein lysine deacetylase activity / positive regulation of signaling receptor activity / regulation of endopeptidase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / negative regulation of gene expression, epigenetic / response to ionizing radiation / embryonic digit morphogenesis / positive regulation of oligodendrocyte differentiation / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / entrainment of circadian clock by photoperiod / eyelid development in camera-type eye / oligodendrocyte differentiation / E-box binding / odontogenesis of dentin-containing tooth / locomotor rhythm / RNA Polymerase I Transcription Initiation / histone deacetylase complex / SUMOylation of transcription factors / 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 / negative regulation of intrinsic apoptotic signaling pathway / MECP2 regulates neuronal receptors and channels / negative regulation of canonical NF-kappaB signal transduction / core promoter sequence-specific DNA 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 / promoter-specific chromatin binding / HDACs deacetylate histones / hippocampus development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / neuron differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / transcription corepressor activity / double-strand break repair / p53 binding / nuclear envelope / chromatin organization / Factors involved in megakaryocyte development and platelet production / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription coactivator activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||||||||||||||
Authors | Millard, C.J. / Robertson, N.S. / Watson, P.J. / Jameson, A.G. / Schwabe, J.W.R. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Nat Commun / Year: 2016 Title: Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Authors: Watson, P.J. / Millard, C.J. / Riley, A.M. / Robertson, N.S. / Wright, L.C. / Godage, H.Y. / Cowley, S.M. / Jamieson, A.G. / Potter, B.V. / Schwabe, J.W. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5icn.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5icn.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 5icn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5icn ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5icn | HTTPS FTP |
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-Related structure data
Related structure data | 4bkxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 22165.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTA1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q13330 |
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#2: Protein | Mass: 43203.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1, RPD3L1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q13547, histone deacetylase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 984.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-IHP / Mass: 660.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C6H18O24P6 / Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC1 / Plasmid: pcDNA3 / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human) |
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#5: Chemical | ChemComp-ZN / |
#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→93.4 Å / Num. obs: 13008 / % possible obs: 93.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.3 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BKX Resolution: 3.3→93.4 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.759 / SU B: 41.5 / SU ML: 0.643 / Cross valid method: THROUGHOUT / ESU R Free: 0.617 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.069 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→93.4 Å
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Refine LS restraints |
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