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

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Basic information

Entry
Database: PDB / ID: 6ogk
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*(5CM)P*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 / negative regulation of dendrite extension / biogenic amine metabolic process / 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 / cellular response to potassium ion / glucocorticoid metabolic process / ventricular system development / positive regulation of microtubule nucleation / unmethylated CpG binding / oligodendrocyte development / 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 / positive regulation of dendritic spine development / Loss of phosphorylation of MECP2 at T308 / response to ionizing radiation / regulation of synapse organization / lung alveolus development / spinal cord development / dendrite development / glutamine metabolic process / startle response / negative regulation of blood vessel endothelial cell migration / social behavior / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / long-term memory / behavioral fear response / glial cell proliferation / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / 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 / molecular condensate scaffold activity / histone reader activity / cerebellum development / adult locomotory behavior / negative regulation of angiogenesis / post-embryonic development / response to cocaine / long-term synaptic potentiation / promoter-specific chromatin binding / hippocampus development / response to lead ion / visual learning / protein localization / cerebral cortex development / chromatin DNA binding / histone deacetylase binding / transcription corepressor activity / response to estradiol / gene expression / heart development / postsynapse / negative regulation of neuron apoptotic process / nucleic acid binding / response to hypoxia / molecular adaptor activity / 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: 1.65 Å
AuthorsLei, M. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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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
D: DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*CP*TP*CP*CP*G)-3')
C: DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,65121
Polymers18,6103
Non-polymers4018
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology, pdb entry 3c2i
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-12 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.470, 51.976, 66.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 11269.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-RIL / References: UniProt: P51608

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DNA chain , 2 types, 2 molecules DC

#2: DNA chain DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*CP*TP*CP*CP*G)-3')


Mass: 3597.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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)

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Non-polymers , 3 types, 74 molecules

#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 50% precipitant mix 4, 0.1M buffer system 1, 0.06M divalents (morpheus A4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.6→40.91 Å / Num. obs: 18969 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 17.5 / Num. measured all: 115783 / 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
1.6-1.634.11.83536508910.3660.9822.0920.797.3
8.78-40.914.80.01472615010.0070.01682.599.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 6c1y

6c1y


Resolution: 1.65→40.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.003 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2552 1773 10.2 %
Rwork0.2259 --
obs0.2289 15648 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.81 Å2 / Biso mean: 29.887 Å2 / Biso min: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å2-0 Å2
2---1.75 Å20 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.65→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms585 487 18 56 1146
Biso mean--29.06 28.52 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121159
X-RAY DIFFRACTIONr_bond_other_d0.0030.018805
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.4451678
X-RAY DIFFRACTIONr_angle_other_deg1.5242.0851883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.407575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02722.18832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.813154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02990
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02262
X-RAY DIFFRACTIONr_mcbond_it1.0361.947303
X-RAY DIFFRACTIONr_mcbond_other1.0371.943302
X-RAY DIFFRACTIONr_mcangle_it1.6492.905377
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 139 -
Rwork0.339 1141 -
all-1280 -
obs--99.92 %
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)
11.2305-0.18740.16713.8901-1.41313.85380.03350.1408-0.0986-0.17740.06050.0330.04920.008-0.09390.00980.0057-0.00480.0475-0.02030.012418.91214.70366.89
23.7879-2.4782-2.05762.74770.07562.6501-0.2685-0.2671-0.07910.08210.2271-0.03010.203-0.06510.04130.02640.02980.00920.1730.08290.091519.21567.912922.1422
36.6317-0.40822.06053.4296-0.54832.3318-0.1509-0.03690.47350.10830.0891-0.0688-0.0933-0.0830.06180.027-0.0356-0.02130.08820.01860.051420.169.468821.9732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 165
2X-RAY DIFFRACTION2D1 - 12
3X-RAY DIFFRACTION3C1 - 12

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