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Yorodumi- PDB-1mm3: Solution structure of the 2nd PHD domain from Mi2b with C-termina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mm3 | ||||||
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Title | Solution structure of the 2nd PHD domain from Mi2b with C-terminal loop replaced by corresponding loop from WSTF | ||||||
Components | Mi2-beta(Chromodomain helicase-DNA-binding protein 4) and transcription factor WSTF | ||||||
Keywords | DNA binding protein/Transcription / PHD / zinc finger / protein scaffold / DNA binding protein-Transcription COMPLEX | ||||||
Function / homology | Function and homology information cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / helicase activity / Regulation of PTEN gene transcription / HDACs deacetylate histones / transcription coregulator binding / double-strand break repair via homologous recombination / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Kwan, A.H.Y. / Gell, D.A. / Verger, A. / Crossley, M. / Matthews, J.M. / Mackay, J.P. | ||||||
Citation | Journal: structure / Year: 2003 Title: Engineering a Protein Scaffold from a PHD Finger Authors: Kwan, A.H.Y. / Gell, D.A. / Verger, A. / Crossley, M. / Matthews, J.M. / Mackay, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mm3.cif.gz | 356.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mm3.ent.gz | 294.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mm3 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mm3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6774.832 Da / Num. of mol.: 1 / Fragment: residues 1-61 Source method: isolated from a genetically manipulated source Details: the C-terminal loop (residue 37-49) was replaced by corresponding loop from WSTF. Source: (gene. exp.) Homo sapiens (human) / Gene: CHD4 / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14839, GenBank: 4049922 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined mostly using standard 2D homonuclear techniques |
-Sample preparation
Details | Contents: 1mM Mi2-phd2-L2wstf protein, 1mM DTT, 10mM sodium phosphate buffer (pH 7.5), 150mM NaCl, 95% H2O, 5% D2O Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 150mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: Structure calculations were performed using the package ARIA1.1 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 968 unambiguous NOE-derived distance ...Details: Structure calculations were performed using the package ARIA1.1 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 968 unambiguous NOE-derived distance constraints, 90 sets of ambiguous NOE-derived distance constraints and 37 additional dihedral angle restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |