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- PDB-1d9n: SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYL... -

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Basic information

Entry
Database: PDB / ID: 1d9n
TitleSOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1
ComponentsMETHYL-CPG-BINDING PROTEIN MBD1
KeywordsGENE REGULATION / MBD / METHYL-CPG / PCM1 / METHYLATION / DNA BINDING DOMAIN
Function / homology
Function and homology information


double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / epigenetic regulation of gene expression / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation ...double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / epigenetic regulation of gene expression / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation / nuclear matrix / response to estradiol / transcription by RNA polymerase II / nuclear speck / response to xenobiotic stimulus / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily ...Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / 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 domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / STRUCTURE CALCULATIONS WERE PERFORMED FOLLOWING SIMULATED ANNEALING PROTOCOLS USING X-PLOR 3.8.
AuthorsOhki, I. / Shimotake, N. / Fujita, N. / Nakao, M. / Shirakawa, M.
Citation
Journal: EMBO J. / Year: 1999
Title: Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1.
Authors: Ohki, I. / Shimotake, N. / Fujita, N. / Nakao, M. / Shirakawa, M.
#1: Journal: Nat.Genet. / Year: 1997
Title: A Component of the Transcriptional Repressor MeCP1 Shares a Motif with DNA Methyltransferase and HRX Proteins
Authors: Cross, S.H. / Meehan, R.R. / Nan, X. / Bird, A.
#2: Journal: Mol.Cell.Biol. / Year: 1999
Title: Methylation-mediated Transcriptional Silencing in Euchromatin by Methyl-CpG Binding Protein MBD1 Isoforms
Authors: Fujita, N. / Takebayashi, S. / Okumura, K. / Kudo, S. / Chiba, T. / Saya, H. / Nakao, M.
History
DepositionOct 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYL-CPG-BINDING PROTEIN MBD1


Theoretical massNumber of molelcules
Total (without water)8,5171
Polymers8,5171
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)25 / 125structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein METHYL-CPG-BINDING PROTEIN MBD1


Mass: 8516.751 Da / Num. of mol.: 1 / Fragment: METHYL-CPG-BINDING DOMAIN OF MBD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: Q9UIS9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1314D 13C/13C-SEPARATED NOESY
1414D 13C/15N-SEPARATED NOESY
151HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTI-DIMENSIONAL HETERONUCLEAR NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 1.3MM MBD U-15N,13C; 20MM PHOSPHATE BUFFER; 50MM KCL; 5MM DTT
Sample conditionsIonic strength: 50mM KCL / pH: 6.5 / Pressure: 1 ATMOSPHERE / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX5002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7DELAGLIOprocessing
PIPP97NOVGARRETTdata analysis
X-PLOR3.8BRUNGERrefinement
RefinementMethod: STRUCTURE CALCULATIONS WERE PERFORMED FOLLOWING SIMULATED ANNEALING PROTOCOLS USING X-PLOR 3.8.
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1270 NOE CONSTRAINTS, 44 DIHEDRAL ANGLE CONSTRAINTS AND 15 HYDROGEN BONDS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 25

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