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- PDB-1ig4: Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1... -

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Basic information

Entry
Database: PDB / ID: 1ig4
TitleSolution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA
Components
  • 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
  • Methyl-CpG Binding Protein
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / ALPHA-BETA / DOUBLE HELIX / RECOGNITION VIA BETA-SHEET / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


double-stranded methylated DNA binding / unmethylated CpG binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / SUMOylation of transcription cofactors / nuclear matrix / chromosome / transcription by RNA polymerase II / nuclear speck / negative regulation of DNA-templated transcription ...double-stranded methylated DNA binding / unmethylated CpG binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / SUMOylation of transcription cofactors / nuclear matrix / chromosome / transcription by RNA polymerase II / nuclear speck / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / 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
DNA / DNA (> 10) / 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.
AuthorsOhki, I. / Shimotake, N. / Fujita, N. / Jee, J.-G. / Ikegami, T. / Nakao, M. / Shirakawa, M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.
Authors: Ohki, I. / Shimotake, N. / Fujita, N. / Jee, J. / Ikegami, T. / Nakao, M. / Shirakawa, M.
#1: 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.
#2: 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.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
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
B: 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
C: 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
A: Methyl-CpG Binding Protein


Theoretical massNumber of molelcules
Total (without water)15,8703
Polymers15,8703
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'


Mass: 3676.431 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Methyl-CpG Binding Protein


Mass: 8516.751 Da / Num. of mol.: 1 / Fragment: Methyl-CpG-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD1 / 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
1114D 13C/15N-separated NOESY
1224D 13C-separated NOESY
1333D 15N-separated NOESY
1423D 13C-filtered 13C-separated NOESY
153HNHA
NMR detailsText: The structure was determined using multi-dimensional heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer90% H2O/10% D2O
21.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer100% D2O
31mM MBD1(U-15N)-DNA Complex; 20mM phosphate buffer90% H2O/10% D2O
Sample conditionspH: 6.5 / 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
NMRPipe1.8Delaglioprocessing
PIPP4.0.4Garrettdata analysis
NMRView4Johnsondata analysis
X-PLOR3.8Brungerrefinement
RefinementMethod: Structure calculations were performed following simulated annealing protocols using X-PLOR.
Software ordinal: 1
Details: The structure was determined from a total of 2,022 distance and dihedral angle restraints, including 91 intermolecular NOE restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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