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- PDB-6ogj: MeCP2 MBD in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6ogj
TitleMeCP2 MBD in complex with DNA
Components
  • DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*TP*AP*CP*AP*CP*TP*CP*CP*G)-3')
  • Methyl-CpG-binding protein 2MECP2
KeywordsDNA BINDING PROTEIN/DNA / MBD / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 / nervous system process involved in regulation of systemic arterial blood pressure / proprioception / : / negative regulation of primary miRNA processing / negative regulation of smooth muscle cell differentiation / MECP2 regulates transcription of neuronal ligands / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of dendritic spine development / Transcriptional Regulation by MECP2 / inositol metabolic process / regulation of respiratory gaseous exchange by nervous system process / double-stranded methylated DNA binding / thalamus development / genomic imprinting / positive regulation of microtubule nucleation / glucocorticoid metabolic process / ventricular system development / cellular response to potassium ion / oligodendrocyte development / unmethylated CpG binding / phosphatidylcholine metabolic process / positive regulation of synaptic plasticity / respiratory gaseous exchange by respiratory system / olfactory bulb development / striatum development / positive regulation of dendrite extension / response to other organism / siRNA binding / neuron maturation / methyl-CpG binding / MECP2 regulates transcription factors / Loss of phosphorylation of MECP2 at T308 / response to ionizing radiation / lung alveolus development / spinal cord development / positive regulation of dendritic spine development / regulation of synapse organization / glutamine metabolic process / startle response / dendrite development / social behavior / negative regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / behavioral fear response / glial cell proliferation / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / long-term memory / heterochromatin formation / MECP2 regulates neuronal receptors and channels / four-way junction DNA binding / positive regulation of glial cell proliferation / Notch signaling pathway / sensory perception of pain / synapse assembly / excitatory postsynaptic potential / histone reader activity / cerebellum development / negative regulation of angiogenesis / molecular condensate scaffold activity / adult locomotory behavior / post-embryonic development / response to cocaine / long-term synaptic potentiation / promoter-specific chromatin binding / hippocampus development / response to lead ion / visual learning / protein localization / chromatin DNA binding / cerebral cortex development / histone deacetylase binding / transcription corepressor activity / response to estradiol / gene expression / heart development / postsynapse / negative regulation of neuron apoptotic process / nucleic acid binding / molecular adaptor activity / response to hypoxia / protein domain specific binding
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLei, M. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochim Biophys Acta Gene Regul Mech / Year: 2019
Title: Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain.
Authors: Lei, M. / Tempel, W. / Chen, S. / Liu, K. / Min, J.
History
DepositionApr 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Oct 11, 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: Methyl-CpG-binding protein 2
D: DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*TP*AP*CP*AP*CP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)29,68612
Polymers29,6864
Non-polymers08
Water73941
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology, pdb entry 3c2i
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.723, 90.181, 40.524
Angle α, β, γ (deg.)90.000, 92.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyl-CpG-binding protein 2 / MECP2 / MeCp2


Mass: 11179.503 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-RIL / References: UniProt: P51608
#2: DNA chain DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3')


Mass: 3743.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*TP*AP*CP*AP*CP*TP*CP*CP*G)-3')


Mass: 3583.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.84 Å3/Da / Density % sol: 33.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 2000 MME, 0.2M potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→45.09 Å / Num. obs: 19585 / % possible obs: 98.6 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Net I/σ(I): 12 / Num. measured all: 65521 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8331.111343111290.4060.7321.3360.994.1
8.99-45.093.30.0215561710.9990.0130.02540.199

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 6c1y

6c1y


Resolution: 1.8→45.09 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.441 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.144
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2562 1109 5.7 %
Rwork0.2261 --
obs0.2278 18390 98.5 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.24 Å2 / Biso mean: 37.548 Å2 / Biso min: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20.16 Å2
2--4.04 Å20 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 1.8→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 485 8 41 1703
Biso mean--36.07 38.54 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121743
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181309
X-RAY DIFFRACTIONr_angle_refined_deg1.51.4912469
X-RAY DIFFRACTIONr_angle_other_deg1.3271.8813033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.18122.03754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38315164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.315156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_mcbond_it1.0922.445633
X-RAY DIFFRACTIONr_mcbond_other1.0912.447634
X-RAY DIFFRACTIONr_mcangle_it1.7993.66789
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 98 -
Rwork0.324 1339 -
all-1437 -
obs--96.06 %
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)
13.6381-0.80730.4672.9303-0.68462.43030.0108-0.0937-0.2168-0.0531-0.0299-0.0730.16310.17820.0190.2081-0.01690.00840.0426-0.01070.16644.92674.91361.4161
23.11490.16630.4741.62140.09711.62730.03020.05230.49780.0418-0.0101-0.055-0.25140.0169-0.02010.26880.01260.0070.00210.01320.28680.222833.396318.0692
30.5182-0.5079-0.39460.56790.7064.03250.1077-0.03290.0325-0.0520.0443-0.0184-0.19030.1696-0.1520.208-0.0097-0.00580.06-0.02140.17041.739219.11991.6989
40.7942-0.8052-1.08470.98820.67784.65780.1238-0.03490.1157-0.09630.1343-0.130.08160.0695-0.2580.2160.0115-0.00210.1083-0.00140.13770.792319.40861.7873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 169
2X-RAY DIFFRACTION2B87 - 169
3X-RAY DIFFRACTION3D1 - 12
4X-RAY DIFFRACTION4C1 - 12

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