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- PDB-3c2i: The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c2i | ||||||
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Title | The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF | ||||||
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Function / homology | ![]() trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : ...trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / negative regulation of dendrite extension / principal sensory nucleus of trigeminal nerve development / cardiolipin metabolic process / negative regulation of locomotion involved in locomotory behavior / Loss of MECP2 binding ability to 5mC-DNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ho, K.L. / McNae, I.W. / Schmiedeberg, L. / Klose, R.J. / Bird, A.P. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: MeCP2 binding to DNA depends upon hydration at methyl-CpG Authors: Ho, K.L. / McNae, I.W. / Schmiedeberg, L. / Klose, R.J. / Bird, A.P. / Walkinshaw, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 11281.381 Da / Num. of mol.: 1 / Fragment: UNP residues 77-167, Human MeCP2 MBD domain / Mutation: A140(MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 6138.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
#3: DNA chain | Mass: 6156.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.33 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 26% PEG2000, 0.2M Ammonium acetate, 0.01M Mg acetate, 0.05M Na cacodylate pH6.5, 0.002M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2006 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→48.795 Å / Num. all: 7122 / Num. obs: 7122 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 84.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 3.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.5 Å / D res low: 1000 Å / FOM : 0.25 / Reflection: 7115 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set site |
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Phasing MAD shell |
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Phasing dm | FOM : 0.53 / FOM acentric: 0.53 / FOM centric: 0.55 / Reflection: 7115 / Reflection acentric: 6648 / Reflection centric: 467 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.076 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→23.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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