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- PDB-6c1y: mbd of human mecp2 in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 6c1y
Titlembd of human mecp2 in complex with methylated DNA
Components
  • 12-mer DNA
  • Methyl-CpG-binding protein 2
KeywordsDNA BINDING PROTEIN/DNA / mbd / dna methylation / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of retrograde dense core granule transport / negative regulation of respiratory gaseous exchange / positive regulation of branching morphogenesis of a nerve / regulation of action potential firing threshold / trans-synaptic signaling by BDNF / positive regulation of anterograde dense core granule transport / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling ...Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of retrograde dense core granule transport / negative regulation of respiratory gaseous exchange / positive regulation of branching morphogenesis of a nerve / regulation of action potential firing threshold / trans-synaptic signaling by BDNF / positive regulation of anterograde dense core granule transport / catecholamine secretion / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / cardiolipin metabolic process / principal sensory nucleus of trigeminal nerve development / 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 dendrite extension / negative regulation of primary miRNA processing / MECP2 regulates transcription of neuronal ligands / negative regulation of smooth muscle cell differentiation / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of dendritic spine development / double-stranded methylated DNA binding / Transcriptional Regulation by MECP2 / regulation of respiratory gaseous exchange by nervous system process / ventricular cardiac muscle tissue development / phosphatidylcholine metabolic process / genomic imprinting / inositol metabolic process / glucocorticoid metabolic process / ventricular system development / unmethylated CpG binding / positive regulation of synaptic plasticity / respiratory gaseous exchange by respiratory system / positive regulation of microtubule nucleation / thalamus development / olfactory bulb development / oligodendrocyte development / positive regulation of dendrite extension / cellular response to potassium ion / striatum development / response to other organism / siRNA binding / neuron maturation / glutamine metabolic process / methyl-CpG binding / response to alcohol / MECP2 regulates transcription factors / Loss of phosphorylation of MECP2 at T308 / positive regulation of dendritic spine development / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / spinal cord development / lung alveolus development / regulation of synapse organization / startle response / social behavior / dendrite development / negative regulation of astrocyte differentiation / negative regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / long-term memory / behavioral fear response / glial cell proliferation / heterochromatin / synapse assembly / four-way junction DNA binding / Nuclear events stimulated by ALK signaling in cancer / MECP2 regulates neuronal receptors and channels / positive regulation of glial cell proliferation / Notch signaling pathway / sensory perception of pain / cerebellum development / negative regulation of angiogenesis / adult locomotory behavior / hippocampus development / post-embryonic development / histone reader activity / excitatory postsynaptic potential / promoter-specific chromatin binding / response to cocaine / molecular condensate scaffold activity / response to lead ion / visual learning / cerebral cortex development / chromatin DNA binding / long-term synaptic potentiation / histone deacetylase binding / transcription corepressor activity / intracellular protein localization / heterochromatin formation / response to estradiol / gene expression / molecular adaptor activity / negative regulation of neuron apoptotic process / nucleic acid binding / response to hypoxia / postsynapse / 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: 2.3 Å
AuthorsLiu, K. / Bian, C. / Tempel, W. / Wernimont, A.K. / 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
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: 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 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-CpG-binding protein 2
B: Methyl-CpG-binding protein 2
D: 12-mer DNA
C: 12-mer DNA
F: 12-mer DNA
E: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)34,2849
Polymers34,2846
Non-polymers03
Water00
1
A: Methyl-CpG-binding protein 2
D: 12-mer DNA
C: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)17,1424
Polymers17,1423
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-10 kcal/mol
Surface area7680 Å2
MethodPISA
2
B: Methyl-CpG-binding protein 2
F: 12-mer DNA
E: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)17,1425
Polymers17,1423
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-6 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.753, 47.359, 54.623
Angle α, β, γ (deg.)68.150, 89.830, 65.980
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C
13D
23F
14D
24E
15C
25F
16C
26E
17F
27E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA92 - 16214 - 84
21GLYGLYARGARGBB92 - 16214 - 84
12DGDGDCDCDC1 - 121 - 12
22DGDGDCDCCD1 - 121 - 12
13DGDGDCDCDC1 - 121 - 12
23DGDGDCDCFE1 - 121 - 12
14DGDGDCDCDC1 - 121 - 12
24DGDGDCDCEF1 - 121 - 12
15DGDGDCDCCD1 - 121 - 12
25DGDGDCDCFE1 - 121 - 12
16DGDGDCDCCD1 - 121 - 12
26DGDGDCDCEF1 - 121 - 12
17DGDGDCDCFE1 - 121 - 12
27DGDGDCDCEF1 - 121 - 12

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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


Mass: 9785.024 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MECP2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P51608
#2: DNA chain
12-mer DNA


Mass: 3678.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic dna / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 25% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→39.85 Å / Num. obs: 14585 / % possible obs: 96.3 % / Redundancy: 2.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.06 / Rrim(I) all: 0.091 / Net I/σ(I): 10.1 / Num. measured all: 31664 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.380.449261712620.7180.3970.6012.484.2
8.91-39.850.0475482550.9830.0440.06530.596.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Protein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.

3c2i


Resolution: 2.3→39.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 25.521 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.262
Details: phenix.refine was used at intermediate stages of refinement. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflection
Rfree0.2857 785 5.4 %
Rwork0.2306 --
obs0.2334 13799 96.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.59 Å2 / Biso mean: 65.544 Å2 / Biso min: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å2-1.93 Å21.86 Å2
2--1.74 Å2-2.26 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.3→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 976 3 0 2069
Biso mean--42.92 --
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0162210
X-RAY DIFFRACTIONr_bond_other_d0.0030.021534
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.613196
X-RAY DIFFRACTIONr_angle_other_deg1.31633576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81923.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15715171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.612156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_mcbond_it2.2945.098566
X-RAY DIFFRACTIONr_mcbond_other2.2965.098565
X-RAY DIFFRACTIONr_mcangle_it3.4727.638704
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A40060.09
12B40060.09
21D20800.03
22C20800.03
31D20380.08
32F20380.08
41D20500.06
42E20500.06
51C20300.09
52F20300.09
61C20700.05
62E20700.05
71F20120.1
72E20120.1
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 96 -
Rwork0.35 837 -
all-933 -
obs--83.45 %
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)
12.13351.5150.91375.15851.19463.50520.03030.30330.2144-0.3564-0.05110.0293-0.4348-0.05230.02080.1847-0.04370.05280.1540.01180.0363-19.0698-3.8257-1.7757
21.4423-0.035-0.4222.6151-1.26655.26670.0555-0.0616-0.3840.1817-0.06230.13320.60870.19690.00680.2112-0.07660.01670.1129-0.02150.1193-1.1211.1002-19.1937
34.37890.0552-1.71273.39560.832.6672-0.0899-0.1053-0.33710.15360.03740.0220.17590.09420.05250.0489-0.06260.01940.1447-0.02290.0467-19.0327-16.71585.5462
45.8765-2.21260.81413.15650.44611.8385-0.2925-0.1689-0.13470.13250.14740.07040.13860.07250.14520.072-0.0219-0.01420.1505-0.00440.0952-19.3406-15.45966.7377
55.71950.2250.31792.34920.43171.9706-0.02630.03750.5236-0.0157-0.00080.0588-0.1253-0.01570.0270.0204-0.03550.01340.1689-0.03940.068-2.534825.7439-23.6403
66.4529-0.89941.06751.979-0.89552.2131-0.0652-0.25440.06560.0463-0.02370.03570.012-0.03150.08890.05270.00740.04710.1582-0.06830.0797-2.636725.5056-22.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 162
2X-RAY DIFFRACTION2B92 - 162
3X-RAY DIFFRACTION3D1 - 12
4X-RAY DIFFRACTION4C1 - 12
5X-RAY DIFFRACTION5F1 - 12
6X-RAY DIFFRACTION6E1 - 12

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