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Yorodumi- PDB-1qk9: The solution structure of the domain from MeCP2 that binds to met... -
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-Basic information
Entry | Database: PDB / ID: 1qk9 | ||||||
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Title | The solution structure of the domain from MeCP2 that binds to methylated DNA | ||||||
Components | METHYL-CPG-BINDING PROTEIN 2 | ||||||
Keywords | METHYL-CPG-BINDING PROTEIN / SOLUTION STRUCTURE / METHYLATED DNA / METHYL CYTOSINE / MBD | ||||||
Function / homology | Function and homology information trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling ...trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / principal sensory nucleus of trigeminal nerve development / cardiolipin metabolic process / negative regulation of dendrite extension / negative regulation of locomotion involved in locomotory behavior / MECP2 regulates transcription factors / Loss of MECP2 binding ability to 5mC-DNA / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / negative regulation of primary miRNA processing / MECP2 regulates transcription of neuronal ligands / negative regulation of smooth muscle cell differentiation / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of dendritic spine development / Transcriptional Regulation by MECP2 / regulation of respiratory gaseous exchange by nervous system process / double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / inositol metabolic process / genomic imprinting / phosphatidylcholine metabolic process / thalamus development / positive regulation of microtubule nucleation / glucocorticoid metabolic process / ventricular system development / cellular response to potassium ion / unmethylated CpG binding / positive regulation of synaptic plasticity / respiratory gaseous exchange by respiratory system / oligodendrocyte development / olfactory bulb development / positive regulation of dendrite extension / striatum development / response to other organism / siRNA binding / neuron maturation / methyl-CpG binding / negative regulation of blood vessel endothelial cell migration / Loss of phosphorylation of MECP2 at T308 / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / spinal cord development / positive regulation of dendritic spine development / lung alveolus development / regulation of synapse organization / histone reader activity / glutamine metabolic process / startle response / dendrite development / positive regulation of glial cell proliferation / social behavior / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / behavioral fear response / glial cell proliferation / heterochromatin / long-term memory / Nuclear events stimulated by ALK signaling in cancer / negative regulation of angiogenesis / MECP2 regulates neuronal receptors and channels / four-way junction DNA binding / Notch signaling pathway / sensory perception of pain / synapse assembly / cerebellum development / adult locomotory behavior / excitatory postsynaptic potential / post-embryonic development / molecular condensate scaffold activity / response to cocaine / promoter-specific chromatin binding / hippocampus development / long-term synaptic potentiation / response to lead ion / visual learning / heterochromatin formation / chromatin DNA binding / cerebral cortex development / histone deacetylase binding / transcription corepressor activity / protein localization / response to estradiol / gene expression / nucleic acid binding / negative regulation of neuron apoptotic process / postsynapse / molecular adaptor activity / response to hypoxia / protein domain specific binding / negative regulation of gene expression Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Wakefield, R.I.D. / Smith, B.O. / Nan, X. / Free, A. / Soteriou, A. / Uhrin, D. / Bird, A.P. / Barlow, P.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The Solution Structure of the Domain from Mecp2 that Binds to Methylated DNA Authors: Wakefield, R.I.D. / Smith, B.O. / Nan, X. / Free, A. / Soteriou, A. / Uhrin, D. / Bird, A.P. / Barlow, P.N. #1: Journal: Mol.Cell.Biol. / Year: 1998 Title: Identification and Characterisation of a Family of Mammalian Methyl-Cpg Binding Proteins Authors: Hendrich, B. / Bird, A.P. #2: Journal: Nature / Year: 1998 Title: Transcriptional Repression by the Methyl-Cpg Binding Protein Mecp2 Involves a Histone Deacetylase Complex Authors: Nan, X.S. / Ng, H.-H. / Johnson, C.A. / Laherty, C.D. / Turner, B.M. / Eisenmann, R.N. / Bird, A. #3: Journal: Cancer Surv. / Year: 1996 Title: The relationship of DNA methylation to cancer. Authors: Bird, A.P. #4: Journal: J.Mol.Biol. / Year: 1995 Title: Calculation of Protein Structures with Ambiguous Distance Restraints Automated Assignment of Ambiguous Noe Crosspeaks and Disulfide Connectivities Authors: Nilges, M. #5: Journal: Cell(Cambridge,Mass.) / Year: 1991 Title: DNA Methylation Inhibits Transcription Indirectly Via a Methyl-Cpg Binding Protein Authors: Boyes, J. / Bird, A.P. #6: Journal: Nature / Year: 1986 Title: Cpg-Rich Islands and the Function of DNA Methylation Authors: Bird, A.P. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qk9.cif.gz | 781 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qk9.ent.gz | 653.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qk9_validation.pdf.gz | 347.1 KB | Display | wwPDB validaton report |
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Full document | 1qk9_full_validation.pdf.gz | 583.8 KB | Display | |
Data in XML | 1qk9_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 1qk9_validation.cif.gz | 87.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qk9 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qk9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10261.530 Da / Num. of mol.: 1 / Fragment: MCPG BINDING DOMAIN OF MECP2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET6HMBD / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51608 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 90% H2O / 10% D2O |
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Sample conditions | pH: 6 / Temperature: 291 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: AMBIGUOUS DISTANCE RESTRAINTS WERE USED SEE M.NILGES CITATION | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 30 / Conformers submitted total number: 28 |