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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 | ||||||
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Title | Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / ALPHA-BETA / DOUBLE HELIX / RECOGNITION VIA BETA-SHEET / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / SUMOylation of transcription cofactors / epigenetic regulation of gene expression / response to cocaine / response to nutrient levels / neuron differentiation ...double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / SUMOylation of transcription cofactors / epigenetic regulation of gene expression / response to cocaine / response to nutrient levels / 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 | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / Structure calculations were performed following simulated annealing protocols using X-PLOR. | ||||||
![]() | Ohki, I. / Shimotake, N. / Fujita, N. / Jee, J.-G. / Ikegami, T. / Nakao, M. / Shirakawa, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 777.1 KB | Display | ![]() |
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PDB format | ![]() | 638.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 377.9 KB | Display | ![]() |
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Full document | ![]() | 685.4 KB | Display | |
Data in XML | ![]() | 61.7 KB | Display | |
Data in CIF | ![]() | 81.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3676.431 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: 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.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using multi-dimensional heteronuclear techniques. |
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Sample preparation
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Sample conditions | pH: 6.5 / Temperature: 303 K | ||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |