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- PDB-3c2i: The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2... -

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Basic information

Entry
Database: PDB / ID: 3c2i
TitleThe Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF
Components
  • DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3')
  • Methyl-CpG-binding protein 2
KeywordsTranscription regulator / water mediated recognition / protein-methylated DNA complex / Asx-ST-motif / Disease mutation / DNA-binding / Nucleus / Phosphoprotein / Repressor
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 / MECP2 regulates transcription of neuronal ligands ...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 / MECP2 regulates transcription of neuronal ligands / negative regulation of smooth muscle cell differentiation / Loss of MECP2 binding ability to the NCoR/SMRT complex / double-stranded methylated DNA binding / Transcriptional Regulation by MECP2 / phosphatidylcholine metabolic process / inositol metabolic process / regulation of respiratory gaseous exchange by nervous system process / glucocorticoid metabolic process / ventricular system development / respiratory gaseous exchange by respiratory system / positive regulation of microtubule nucleation / genomic imprinting / response to other organism / siRNA binding / neuron maturation / 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 / Regulation of MECP2 expression and activity / social behavior / long-term memory / behavioral fear response / glial cell proliferation / heterochromatin / MECP2 regulates neuronal receptors and channels / Nuclear events stimulated by ALK signaling in cancer / synapse assembly / Notch signaling pathway / positive regulation of glial cell proliferation / sensory perception of pain / negative regulation of angiogenesis / cerebellum development / adult locomotory behavior / histone reader activity / excitatory postsynaptic potential / post-embryonic development / promoter-specific chromatin binding / molecular condensate scaffold activity / visual learning / long-term synaptic potentiation / transcription corepressor activity / intracellular protein localization / heterochromatin formation / molecular adaptor activity / negative regulation of neuron apoptotic process / gene expression / nucleic acid binding / response to hypoxia / postsynapse / negative regulation of gene expression / negative regulation of DNA-templated transcription / mRNA binding / centrosome / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / 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 / SAD / Resolution: 2.5 Å
AuthorsHo, K.L. / McNae, I.W. / Schmiedeberg, L. / Klose, R.J. / Bird, A.P. / Walkinshaw, M.D.
CitationJournal: Mol.Cell / Year: 2008
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
DepositionJan 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-CpG-binding protein 2
B: DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3')
C: DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)23,5753
Polymers23,5753
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-12.7 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.710, 53.600, 65.730
Angle α, β, γ (deg.)90.000, 132.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-CpG-binding protein 2 / MeCP-2 protein / MeCP2


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.) 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(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3')


Mass: 6138.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#3: DNA chain DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3')


Mass: 6156.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 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
IDNameCrystal-IDSol-ID
1PEG200011
2Ammonium acetate11
3Mg acetate11
4Na cacodylate11
5HOH11
6PEG200012
7Ammonium acetate12
8Mg acetate12
9Na cacodylate12
10HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2006 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.645.30.377250559500.37790.7
2.64-2.87.10.3122.3706910000.31299.9
2.8-2.997.50.2053.668639210.205100
2.99-3.237.40.0952.164838710.095100
3.23-3.547.40.0762.158867910.07699.9
3.54-3.957.40.0696.254337300.069100
3.95-4.567.40.0629.947106360.062100
4.56-5.597.40.0698.441235600.069100
5.59-7.917.30.067.731184290.06100
7.91-25.666.70.0569.615672340.05696.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 1000 Å / FOM : 0.25 / Reflection: 7115
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se59.7310.8370.3650.1471.023
2Se600.9710.0240.0520.861
Phasing MAD shell
Resolution (Å)FOM Reflection
9.13-10000.44330
5.72-9.130.5590
4.46-5.720.45759
3.77-4.460.38905
3.33-3.770.291004
3.01-3.330.191129
2.77-3.010.111190
2.58-2.770.061208
Phasing dmFOM : 0.53 / FOM acentric: 0.53 / FOM centric: 0.55 / Reflection: 7115 / Reflection acentric: 6648 / Reflection centric: 467
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-25.6560.940.950.8731726156
4.5-7.10.90.910.7397288389
3.6-4.50.840.850.761222113191
3.1-3.60.640.650.541207113671
2.7-3.10.30.30.2721522038114
2.5-2.70.140.140.151245119946

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→23.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 24.894 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.651 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 331 4.7 %RANDOM
Rwork0.212 ---
obs0.215 7115 98.53 %-
all-7115 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.07 Å2
2--0.3 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms584 816 0 47 1447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211512
X-RAY DIFFRACTIONr_angle_refined_deg1.8482.6282212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.524571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42522.75929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45415107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.077156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02870
X-RAY DIFFRACTIONr_nbd_refined0.2190.2551
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.25
X-RAY DIFFRACTIONr_mcbond_it0.6931.5363
X-RAY DIFFRACTIONr_mcangle_it0.8982576
X-RAY DIFFRACTIONr_scbond_it1.00131553
X-RAY DIFFRACTIONr_scangle_it1.5794.51636
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 22 -
Rwork0.428 442 -
all-464 -
obs--88.38 %

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