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Yorodumi- PDB-4bkx: The structure of HDAC1 in complex with the dimeric ELM2-SANT doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bkx | ||||||
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Title | The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex | ||||||
Components |
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Keywords | TRANSCRIPTION / INOSITOL PHOSPHATE SIGNALLING / ELM2-SANT DOMAIN / HDAC / HDAC1 / HISTONE DEACETYLASE / MTA1 | ||||||
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 / negative regulation by host of viral transcription ...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 / negative regulation by host of viral transcription / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / eyelid development in camera-type eye / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / protein deacetylation / E-box binding / Regulation of MITF-M-dependent genes involved in apoptosis / Transcription of E2F targets under negative control by DREAM complex / STAT3 nuclear events downstream of ALK signaling / positive regulation of protein autoubiquitination / histone deacetylase / G0 and Early G1 / DNA methylation-dependent heterochromatin formation / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / SUMOylation of chromatin organization proteins / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of oligodendrocyte differentiation / response to ionizing radiation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / Sin3-type complex / entrainment of circadian clock by photoperiod / oligodendrocyte differentiation / odontogenesis of dentin-containing tooth / locomotor rhythm / RNA Polymerase I Transcription Initiation / histone deacetylase complex / SUMOylation of transcription factors / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / hair follicle placode formation / Regulation of MECP2 expression and activity / NF-kappaB binding / 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 / negative regulation of intrinsic apoptotic signaling pathway / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / negative regulation of canonical NF-kappaB signal transduction / Regulation of TP53 Activity through Acetylation / Regulation of PTEN gene transcription / transcription repressor complex / positive regulation of smooth muscle cell proliferation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / promoter-specific chromatin binding / hippocampus development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / circadian regulation of gene expression / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / heterochromatin formation / neuron differentiation / p53 binding / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / nuclear envelope / double-strand break repair / Factors involved in megakaryocyte development and platelet production / chromatin organization / DNA-binding transcription factor binding / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Millard, C.J. / Watson, P.J. / Celardo, I. / Gordiyenko, Y. / Cowley, S.M. / Robinson, C.V. / Fairall, L. / Schwabe, J.W.R. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Class I Hdacs Share a Common Mechanism of Regulation by Inositol Phosphates. Authors: Millard, C.J. / Watson, P.J. / Celardo, I. / Gordiyenko, Y. / Cowley, S.M. / Robinson, C.V. / Fairall, L. / Schwabe, J.W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bkx.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bkx.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 4bkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bkx_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 4bkx_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4bkx_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4bkx_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bkx ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bkx | HTTPS FTP |
-Related structure data
Related structure data | 4a69S 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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Details | DIMER OF A HETERODIMERIC COMPLEX |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19961.213 Da / Num. of mol.: 1 / Fragment: ELM2-SANT Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13330 |
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#2: Protein | Mass: 55178.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13547, histone deacetylase |
-Non-polymers , 4 types, 8 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-ACT / | ||
#5: Chemical | #6: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.8 % / Description: NONE |
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Crystal grow | 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: 0.9778 |
Detector | Date: Oct 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3→76.6 Å / Num. obs: 16916 / % possible obs: 96.7 % / Observed criterion σ(I): 1.8 / Redundancy: 3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A69 Resolution: 3→76.75 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.18 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.23 Å2
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Refinement step | Cycle: LAST / Resolution: 3→76.75 Å
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