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- 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
TitleThe solution structure of the domain from MeCP2 that binds to methylated DNA
ComponentsMETHYL-CPG-BINDING PROTEIN 2
KeywordsMETHYL-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 / negative regulation of dendrite extension / principal sensory nucleus of trigeminal nerve development / cardiolipin metabolic process / negative regulation of locomotion involved in locomotory behavior / 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 / oligodendrocyte development / respiratory gaseous exchange by respiratory system / olfactory bulb development / positive regulation of dendrite extension / striatum development / response to other organism / siRNA binding / neuron maturation / methyl-CpG binding / MECP2 regulates transcription factors / 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 / regulation of synapse organization / lung alveolus development / glutamine metabolic process / startle response / dendrite development / social behavior / negative regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / behavioral fear response / glial cell proliferation / Nuclear events stimulated by ALK signaling in cancer / heterochromatin / long-term memory / heterochromatin formation / MECP2 regulates neuronal receptors and channels / four-way junction DNA binding / positive regulation of glial cell proliferation / Notch signaling pathway / sensory perception of pain / synapse assembly / histone reader activity / excitatory postsynaptic potential / negative regulation of angiogenesis / adult locomotory behavior / cerebellum development / post-embryonic development / molecular condensate scaffold activity / response to cocaine / long-term synaptic potentiation / hippocampus development / promoter-specific chromatin binding / response to lead ion / visual learning / protein localization / chromatin DNA binding / cerebral cortex development / histone deacetylase binding / transcription corepressor activity / response to estradiol / gene expression / postsynapse / negative regulation of neuron apoptotic process / nucleic acid binding / molecular adaptor activity / response to hypoxia / protein domain specific binding / negative regulation of gene expression
Similarity search - Function
Methyl-CpG binding protein MeCP2 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methyl-CpG-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWakefield, 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
DepositionJul 12, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last / _citation.title
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYL-CPG-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)10,2621
Polymers10,2621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 30LOWEST ENERGIES
RepresentativeModel #5

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Components

#1: Protein METHYL-CPG-BINDING PROTEIN 2 / MBD


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HNCA
151HN(CO)CA
161CBCA(CO)NH
171HNCO
181HN(CA)CB
191(H)CCH-TOCSY
1101H(CCO)NH-TOCSY
1111C(CO)NH-TOCSY
112115N-EDITTED HSQC
113113C-EDITTED HSQC
1141HBHA(CO)NH
115115N-EDITTED HSQC-NOESY
116113C-EDITTED HSQC-NOESY

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Sample preparation

DetailsContents: 90% H2O / 10% D2O
Sample conditionspH: 6.0 / Temperature: 291 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
VNMRstructure solution
Azarastructure solution
ANSIGstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: AMBIGUOUS DISTANCE RESTRAINTS WERE USED SEE M.NILGES CITATION
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 30 / Conformers submitted total number: 28

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