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- PDB-7d8k: Solution structure of the methyl-CpG binding domain of MBD6 from ... -

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Basic information

Entry
Database: PDB / ID: 7d8k
TitleSolution structure of the methyl-CpG binding domain of MBD6 from Arabidopsis thaliana
ComponentsMethyl-CpG-binding domain-containing protein 6
KeywordsDNA BINDING PROTEIN / methyl-CpG binding / gene repressor
Function / homology
Function and homology information


nucleolus organizer region / perinucleolar chromocenter / regulatory ncRNA-mediated gene silencing / methyl-CpG binding / plastid / heterochromatin / : / enzyme binding / nucleus
Similarity search - Function
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 domain-containing protein 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsMahana, Y. / Ohki, I. / Walinda, E. / Morimoto, D. / Sugase, K. / Shirakawa, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP16gm0510004 Japan
CitationJournal: Acs Omega / Year: 2022
Title: Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana .
Authors: Mahana, Y. / Ohki, I. / Walinda, E. / Morimoto, D. / Sugase, K. / Shirakawa, M.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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-containing protein 6


Theoretical massNumber of molelcules
Total (without water)7,7711
Polymers7,7711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Methyl-CpG-binding domain-containing protein 6 / MBD06 / Methyl-CpG-binding protein MBD6


Mass: 7770.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MBD6, At5g59380, F2O15.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LTJ1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-15N HSQC
124isotropic13D HNCO
134isotropic13D HN(CA)CO
144isotropic13D CBCA(CO)NH
154isotropic13D HN(CA)CB
164isotropic12D 1H-13C HSQC aliphatic
174isotropic12D 1H-13C HSQC aromatic
184isotropic13D CC(CO)NH
194isotropic13D H(CC)(CO)NH
1104isotropic13D HBHA(CO)NH
1114isotropic13D HBHANH
1124isotropic13D (H)CCH-TOCSY
1134isotropic13D (H)CCH-COSY
1144isotropic12D (HB)CB(CGCD)HD
1154isotropic12D (HB)CB(CGCDCE)HE
1164isotropic13D 1H-15N NOESY
1174isotropic13D 1H-13C NOESY aliphatic
1184isotropic13D 1H-13C NOESY aromatic
1195isotropic22D IPAP 1H-15N HSQC
1203anisotropic22D IPAP 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution41.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O13C/15N sample for assignment and NOESY95% H2O/5% D2O
solution50.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O13C/15N sample for isotropic IPAP95% H2O/5% D2O
solution30.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride, 4 % C12E5, 1.2 % 1-hexanol, 95% H2O/5% D2O13C/15N sample for aligned IPAP95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMAtMBD6 MBD domain[U-13C; U-15N]4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
0.5 mMAtMBD6 MBD domain[U-13C; U-15N]5
20 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
0.5 mMAtMBD6 MBD domain[U-13C; U-15N]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
4 %C12E5natural abundance3
1.2 %1-hexanolnatural abundance3
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II7001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOS+Shen, Delaglio, and Cornilescudata analysis
MagRO-NMRViewKobayashi (MagRO), Johnson and Blevins (NMRView)chemical shift assignment
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospindata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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