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- PDB-5bt2: MeCP2 MBD domain (A140V) in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 5bt2
TitleMeCP2 MBD domain (A140V) in complex with methylated DNA
Components
  • DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')
  • Methyl-CpG-binding protein 2
KeywordsDNA BINDING PROTEIN/DNA / A/T run / MeCP2 / hydration spine / methylated DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5hmC-DNA / trans-synaptic signaling by BDNF / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / cardiolipin metabolic process / Loss of MECP2 binding ability to 5mC-DNA / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / negative regulation of smooth muscle cell differentiation ...Loss of MECP2 binding ability to 5hmC-DNA / trans-synaptic signaling by BDNF / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / cardiolipin metabolic process / Loss of MECP2 binding ability to 5mC-DNA / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / negative regulation of smooth muscle cell differentiation / MECP2 regulates transcription of neuronal ligands / Loss of MECP2 binding ability to the NCoR/SMRT complex / double-stranded methylated DNA binding / phosphatidylcholine metabolic process / inositol metabolic process / glucocorticoid metabolic process / regulation of respiratory gaseous exchange by nervous system process / Transcriptional Regulation by MECP2 / ventricular system development / respiratory gaseous exchange by respiratory system / positive regulation of microtubule nucleation / genomic imprinting / response to other organism / neuron maturation / siRNA binding / glutamine metabolic process / methyl-CpG binding / MECP2 regulates transcription factors / Loss of phosphorylation of MECP2 at T308 / negative regulation of gene expression via chromosomal CpG island methylation / startle response / dendrite development / negative regulation of blood vessel endothelial cell migration / histone reader activity / positive regulation of glial cell proliferation / Regulation of MECP2 expression and activity / social behavior / long-term memory / glial cell proliferation / behavioral fear response / MECP2 regulates neuronal receptors and channels / heterochromatin / Notch signaling pathway / Nuclear events stimulated by ALK signaling in cancer / synapse assembly / sensory perception of pain / cerebellum development / negative regulation of angiogenesis / adult locomotory behavior / post-embryonic development / excitatory postsynaptic potential / promoter-specific chromatin binding / molecular condensate scaffold activity / visual learning / intracellular protein localization / transcription corepressor activity / long-term synaptic potentiation / heterochromatin formation / gene expression / nucleic acid binding / negative regulation of neuron apoptotic process / molecular adaptor activity / response to hypoxia / postsynapse / negative regulation of gene expression / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / centrosome / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Methyl-CpG binding protein MeCP2 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / 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 protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHo, K.L. / Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L.
Funding support Malaysia, 2items
OrganizationGrant numberCountry
Ministry of Higher Education03-10-10-948FR Malaysia
Universiti Putra Malaysia04-02-12-1813RU Malaysia
CitationJournal: Sci Rep / Year: 2016
Title: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.
Authors: Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L. / Ho, K.L.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-CpG-binding protein 2
B: DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')
C: DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,4503
Polymers23,4503
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-14 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.660, 53.490, 65.780
Angle α, β, γ (deg.)90.000, 132.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-CpG-binding protein 2 / MeCp2


Mass: 11155.526 Da / Num. of mol.: 1 / Fragment: MBD domain, UNP residues 77-167 / Mutation: A140V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: P51608
#2: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3')


Mass: 6138.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3')


Mass: 6156.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 2000, 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate
PH range: 6.0-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 10482 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALAdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2I

3c2i


Resolution: 2.2→48.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 13.84 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 525 5 %RANDOM
Rwork0.1746 ---
obs0.1773 9955 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.62 Å2 / Biso mean: 73.464 Å2 / Biso min: 39.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å21.92 Å2
2---3.4 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 2.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 816 0 141 1529
Biso mean---69.46 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141500
X-RAY DIFFRACTIONr_bond_other_d0.0030.021011
X-RAY DIFFRACTIONr_angle_refined_deg1.831.5132198
X-RAY DIFFRACTIONr_angle_other_deg1.37232365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.441570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28723.21428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8515102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.745155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_mcbond_it3.3994.784283
X-RAY DIFFRACTIONr_mcbond_other3.3994.773282
X-RAY DIFFRACTIONr_mcangle_it4.7097.152352
LS refinement shellResolution: 2.182→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 44 -
Rwork0.284 734 -
all-778 -
obs--98.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.92860.315-0.18097.95460.70722.9093-0.0596-0.3707-0.30380.99270.1367-0.82570.14150.2197-0.07710.20540.0437-0.1860.06390.00630.229.222-1.429-17.755
25.1673-0.404-2.92580.60680.26124.1612-0.15340.14120.2714-0.08330.27220.18220.39040.1195-0.11880.0634-0.046-0.0190.21520.03560.16981.6860.63-30.22
34.32010.1296-2.27150.4598-0.5394.2976-0.450.48730.08510.03050.2233-0.01440.5495-0.08590.22670.1359-0.02020.05360.24980.00330.11014.7680.483-33.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 162
2X-RAY DIFFRACTION2B1 - 20
3X-RAY DIFFRACTION3C21 - 40

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