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- PDB-2mb7: Solution structure of MBD3 methylcytosine binding domain -

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Basic information

Entry
Database: PDB / ID: 2mb7
TitleSolution structure of MBD3 methylcytosine binding domain
ComponentsMethyl-CpG-binding domain protein 3
KeywordsTRANSCRIPTION / MBD3 / DNA methylation / NuRD / chromatin
Function / homology
Function and homology information


ventricular cardiac muscle tissue development / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Regulation of TP53 Activity through Acetylation ...ventricular cardiac muscle tissue development / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Regulation of TP53 Activity through Acetylation / response to nutrient levels / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / HDACs deacetylate histones / response to estradiol / in utero embryonic development / Potential therapeutics for SARS / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. ...Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWilliams Jr., D.C. / Scarsdale, J.N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA.
Authors: Cramer, J.M. / Scarsdale, J.N. / Walavalkar, N.M. / Buchwald, W.A. / Ginder, G.D. / Williams, D.C.
History
DepositionJul 26, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 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 domain protein 3


Theoretical massNumber of molelcules
Total (without water)8,3431
Polymers8,3431
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Methyl-CpG-binding domain protein 3 / Methyl-CpG-binding protein MBD3


Mass: 8342.521 Da / Num. of mol.: 1 / Fragment: Methyl-CpG-binding domain (UNP residues 1-70)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: O95983

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5-1.0 mM [U-99% 13C; U-99% 15N] MBD3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: MBD3-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] / Conc. range: 0.5-1.0
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPNVranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, and Lauedata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 528 / NOE intraresidue total count: 102 / NOE long range total count: 160 / NOE medium range total count: 111 / NOE sequential total count: 155 / Protein chi angle constraints total count: 12 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.8 ° / Maximum upper distance constraint violation: 0.48 Å
NMR ensemble rmsDistance rms dev: 0.018 Å / Distance rms dev error: 0.003 Å

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