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- PDB-6c1t: MBD2 in complex with a partially methylated DNA -

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Basic information

Entry
Database: PDB / ID: 6c1t
TitleMBD2 in complex with a partially methylated DNA
Components
  • (12-mer DNA) x 2
  • Methyl-CpG-binding domain protein 2
KeywordsDNA BINDING PROTEIN/DNA / MBD / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / methyl-CpG binding / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway / embryonic organ development / heterochromatin / response to mechanical stimulus / RNA Polymerase I Promoter Opening / response to nutrient levels / NoRC negatively regulates rRNA expression / Wnt signaling pathway / response to estradiol / regulation of cell population proliferation / protein-containing complex assembly / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLei, M. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.
Authors: Liu, K. / Xu, C. / Lei, M. / Yang, A. / Loppnau, P. / Hughes, T.R. / Min, J.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2May 23, 2018Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 2
B: 12-mer DNA
C: 12-mer DNA
D: Methyl-CpG-binding domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,11130
Polymers24,9234
Non-polymers18826
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, see PDB entry 2ky8
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-38 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.473, 36.933, 104.076
Angle α, β, γ (deg.)90.000, 108.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Methyl-CpG-binding domain protein 2 / Demethylase / DMTase / Methyl-CpG-binding protein MBD2


Mass: 8791.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-RIL / References: UniProt: Q9UBB5

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 12-mer DNA


Mass: 3597.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 12-mer DNA


Mass: 3743.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 67 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 24 / Source method: obtained synthetically
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 27% PEG-3350, 0.1 M Bis-Tris, 0.15 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→49.42 Å / Num. obs: 22367 / % possible obs: 99 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Net I/σ(I): 9.8 / Num. measured all: 71924 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.8831.244370512360.340.8281.5010.791.3
9.03-49.422.90.0316362170.9980.020.03727.499.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: currently unpublished model of MBD2-DNA complex

Resolution: 1.84→49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.995 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.126
Details: The identity of the 'sulfate' near Ser-183 is unclear. Similar density was also observed in another MBD2-DNA complex crystal where the crystallization buffer did not include sulfate.
RfactorNum. reflection% reflection
Rfree0.2468 1095 4.9 %
Rwork0.2137 --
obs0.2153 21271 98.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.51 Å2 / Biso mean: 49.509 Å2 / Biso min: 31.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.06 Å2
2--0.01 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.84→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 487 35 41 1559
Biso mean--46.16 44.94 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0171576
X-RAY DIFFRACTIONr_bond_other_d0.0020.021195
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.7012229
X-RAY DIFFRACTIONr_angle_other_deg1.18232771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36821.57938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.662158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02346
X-RAY DIFFRACTIONr_mcbond_it1.3752.957531
X-RAY DIFFRACTIONr_mcbond_other1.3762.953530
X-RAY DIFFRACTIONr_mcangle_it2.0274.418661
LS refinement shellResolution: 1.844→1.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 82 -
Rwork0.336 1428 -
all-1510 -
obs--92.81 %
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)
12.8517-0.97241.31193.7358-1.25996.31250.04450.0091-0.2085-0.26830.08490.09720.312-0.0897-0.12940.1818-0.0658-0.00010.0948-0.00190.0158-15.174526.9201108.8401
28.03484.02730.94623.976-0.32181.8834-0.1763-0.147-0.3687-0.14750.0971-0.04610.0775-0.10420.07920.094-0.02330.03480.1452-0.01150.0586-15.971432.1378124.1032
36.76153.90070.80793.802-0.16140.7873-0.0883-0.17430.2003-0.01730.05380.1574-0.0071-0.15910.03450.1319-0.0570.00130.1569-0.00130.0091-16.192533.4383123.3795
42.24680.0718-1.6755.3269-2.92227.1232-0.0129-0.8720.26770.8714-0.0727-0.066-0.34160.25160.08570.2923-0.0733-0.05020.5024-0.04610.1006-6.020443.8811138.4985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A148 - 215
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D149 - 214

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