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- PDB-8ajr: The Solution Structure of the Triple Mutant Methyl-CpG-Binding Do... -

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Basic information

Entry
Database: PDB / ID: 8ajr
TitleThe Solution Structure of the Triple Mutant Methyl-CpG-Binding Domain from MeCP2
ComponentsMethyl-CpG-binding protein 2
KeywordsGENE REGULATION / Epigenetic modifications / Reader protein / Domain of MeCP2
Function / homology
Function and homology information


trans-synaptic signaling by BDNF / catecholamine secretion / biogenic amine metabolic process / cardiolipin metabolic process / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / negative regulation of smooth muscle cell differentiation / double-stranded methylated DNA binding / phosphatidylcholine metabolic process / inositol metabolic process ...trans-synaptic signaling by BDNF / catecholamine secretion / biogenic amine metabolic process / cardiolipin metabolic process / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / negative regulation of smooth muscle cell differentiation / double-stranded methylated DNA binding / phosphatidylcholine metabolic process / inositol metabolic process / regulation of respiratory gaseous exchange by nervous system process / glucocorticoid metabolic process / respiratory gaseous exchange by respiratory system / ventricular system development / positive regulation of microtubule nucleation / genomic imprinting / response to other organism / siRNA binding / neuron maturation / glutamine metabolic process / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / startle response / dendrite development / histone reader activity / negative regulation of blood vessel endothelial cell migration / positive regulation of glial cell proliferation / social behavior / long-term memory / behavioral fear response / glial cell proliferation / heterochromatin / synapse assembly / Notch signaling pathway / sensory perception of pain / cerebellum development / negative regulation of angiogenesis / adult locomotory behavior / post-embryonic development / excitatory postsynaptic potential / promoter-specific chromatin binding / molecular condensate scaffold activity / visual learning / long-term synaptic potentiation / transcription corepressor activity / intracellular protein localization / heterochromatin formation / gene expression / negative regulation of neuron apoptotic process / response to hypoxia / postsynapse / mRNA binding / centrosome / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytosol
Similarity search - Function
Methyl-CpG binding protein MeCP2 / 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
Similarity search - Domain/homology
Methyl-CpG-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSingh, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity.
Authors: Singh, H. / Das, C.K. / Buchmuller, B.C. / Schafer, L.V. / Summerer, D. / Linser, R.
#1: Journal: Biorxiv / Year: 2022
Title: Epigenetic CpG Duplex Marks Probed by an Evolved DNA Reader via a Well-Tempered Conformational Plasticity
Authors: Singh, H. / Das, C.K. / Buchmuller, B.C. / Eppmann, S. / Schafer, L.V. / Summerer, D. / Linser, R.
History
DepositionJul 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)11,9051
Polymers11,9051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Methyl-CpG-binding protein 2 / MeCp-2 protein / MeCp2


Mass: 11905.288 Da / Num. of mol.: 1 / Mutation: T, A, N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Mecp2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C5LDB3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic12D 1H-15N HSQC
191anisotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-100% 13C; U-100% 15N] MBD, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution20.6 mM [U-100% 15N] MBD, 90% H2O/10% D2O13C_15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMMBD[U-100% 13C; U-100% 15N]1
0.6 mMMBD[U-100% 15N]2
Sample conditionsIonic strength: 100 mM / Label: 13C and 15N / pH: 6 Not defined / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: total restraints 658
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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