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- PDB-6ccg: Crystal structure MBD3 MBD domain in complex with methylated CpG DNA -

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Basic information

Entry
Database: PDB / ID: 6ccg
TitleCrystal structure MBD3 MBD domain in complex with methylated CpG DNA
Components
  • DNA
  • Methyl-CpG-binding domain protein 3
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 ...ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Regulation of TP53 Activity through Acetylation / response to nutrient levels / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / response to estradiol / in utero embryonic development / Potential therapeutics for SARS / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. ...Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / 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 domain protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsLiu, K. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Febs J. / Year: 2019
Title: Structural analyses reveal that MBD3 is a methylated CG binder.
Authors: Liu, K. / Lei, M. / Wu, Z. / Gan, B. / Cheng, H. / Li, Y. / Min, J.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 domain protein 3
B: Methyl-CpG-binding domain protein 3
C: DNA
D: DNA
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)31,66116
Polymers31,6616
Non-polymers010
Water1,58588
1
A: Methyl-CpG-binding domain protein 3
C: DNA
D: DNA


Theoretical massNumber of molelcules
Total (without water)15,8318
Polymers15,8313
Non-polymers05
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-8 kcal/mol
Surface area7700 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 3
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)15,8318
Polymers15,8313
Non-polymers05
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-8 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.270, 36.460, 130.840
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-CpG-binding domain protein 3 / Methyl-CpG-binding protein MBD3


Mass: 8473.716 Da / Num. of mol.: 2 / Fragment: residues 1-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD3 / Plasmid: PET28-GSTLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95983
#2: DNA chain
DNA


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


Num. of mol.: 10 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.8 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG 8000,0.2M magnesium chloride, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.9→35.18 Å / Num. obs: 27299 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 16.7 / Num. measured all: 155271 / Scaling rejects: 12
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
1.9-1.943.71.098649117490.6150.6621.2851.299.8
9.11-35.185.70.02915512720.9990.0140.03354.197.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→35.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.217 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1536 5.6 %thin shells (sftools)
Rwork0.2232 ---
obs0.2247 25763 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 43.018 Å2 / Biso min: 26.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20.33 Å2
2--1.39 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.9→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 976 10 88 2218
Biso mean--41.16 43.7 -
Num. residues----191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0162322
X-RAY DIFFRACTIONr_bond_other_d0.0040.021659
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6333348
X-RAY DIFFRACTIONr_angle_other_deg1.1933872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.5920.18953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30615212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7511518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02533
X-RAY DIFFRACTIONr_mcbond_it1.3612.425578
X-RAY DIFFRACTIONr_mcbond_other1.3622.422577
X-RAY DIFFRACTIONr_mcangle_it2.2023.622722
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 102 -
Rwork0.318 1878 -
all-1980 -
obs--99.9 %
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)
12.65570.6015-0.39773.6366-2.34734.05510.0026-0.1839-0.16340.03330.03960.05730.3074-0.2993-0.04210.25760.03170.01340.14250.00660.0152-23.1226-4.603354.5264
22.6219-0.79890.43913.296-2.20575.08650.01320.21020.153-0.13480.00070.0739-0.2646-0.2219-0.01390.2295-0.03110.00220.1279-0.0020.0164-20.32386.718210.5204
34.1799-4.18190.97484.321-0.74072.15030.10310.04170.3944-0.1403-0.1117-0.28340.07330.08350.00860.23120.08440.02950.1529-0.04790.2028-18.54318.38346.3019
46.1548-2.11471.32762.29120.23220.63810.11160.38470.3274-0.185-0.1887-0.130.00570.02570.07710.21740.08350.06830.18410.00230.0843-18.66687.764844.9913
54.64583.2847-0.39313.1698-0.62851.8201-0.00670.072-0.38440.0589-0.0242-0.16870.00820.04770.03090.1716-0.0611-0.03760.1208-0.05220.122-15.8571-6.295519.0526
66.44412.2223-1.19582.7586-0.23011.36850.0993-0.3761-0.24770.1225-0.1448-0.1035-0.00990.03860.04560.1608-0.0808-0.05550.1577-0.01110.0926-15.9606-5.677720.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 80
2X-RAY DIFFRACTION2B0 - 80
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12

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