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- PDB-6c1u: MBD2 in complex with a deoxy-oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 6c1u
TitleMBD2 in complex with a deoxy-oligonucleotide
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 / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding ...satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / 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 / FOURIER SYNTHESIS / Resolution: 2.3 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,84850
Polymers49,8488
Non-polymers042
Water45025
1
A: Methyl-CpG-binding domain protein 2
B: Methyl-CpG-binding domain protein 2
C: 12-mer DNA
D: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)24,92428
Polymers24,9244
Non-polymers024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Methyl-CpG-binding domain protein 2
F: Methyl-CpG-binding domain protein 2
G: 12-mer DNA
H: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)24,92422
Polymers24,9244
Non-polymers018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.912, 40.015, 105.890
Angle α, β, γ (deg.)84.480, 85.910, 62.770
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 8791.171 Da / Num. of mol.: 4
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
#2: DNA chain 12-mer DNA


Mass: 3759.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 12-mer DNA


Mass: 3582.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 42 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 56.08 % / Mosaicity: 0.33 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG-3350, 0.2 M potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 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: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→35.49 Å / Num. obs: 33843 / % possible obs: 92.6 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.033 / Rrim(I) all: 0.049 / Net I/σ(I): 11.3 / Num. measured all: 64867 / 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
1.99-2.051.70.578284216910.5880.530.7861.163
8.92-35.4920.0237653880.9970.020.03131.993.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.

Resolution: 2.3→35.1 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.714 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 808 3.6 %thin resolution shells (sftools)
Rwork0.2316 ---
obs0.2331 21914 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 48.293 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.83 Å20.98 Å2
2--0.87 Å2-0.78 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 2.3→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 974 42 25 3076
Biso mean--30.47 34.84 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0173176
X-RAY DIFFRACTIONr_bond_other_d0.0020.022407
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.6964484
X-RAY DIFFRACTIONr_angle_other_deg1.21935571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99221.13979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8421519
X-RAY DIFFRACTIONr_chiral_restr0.10.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02717
X-RAY DIFFRACTIONr_mcbond_it1.3533.1131084
X-RAY DIFFRACTIONr_mcbond_other1.3523.1111082
X-RAY DIFFRACTIONr_mcangle_it2.174.6581350
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.266 1698 -
obs--95.82 %
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)
12.7073-1.1763-0.04853.39791.48227.013-0.0229-0.1635-0.00160.18180.1297-0.2299-0.19740.2914-0.10680.0696-0.08960.01450.1923-0.03910.0478-27.750516.3216-25.6641
23.3243-1.1754-3.82051.45530.26758.01060.14740.5741-0.0071-0.602-0.1880.14940.0964-0.38610.04060.3816-0.0498-0.05110.3122-0.02780.0897-45.15398.4864-55.0331
34.24434.36990.4417.37281.68331.6847-0.07110.01780.2648-0.45890.02210.2951-0.30290.12280.0490.0838-0.04590.00250.0787-0.01740.0274-34.93617.9478-39.8557
43.55723.19040.35368.02370.94491.59170.0356-0.03550.0434-0.2222-0.0817-0.3429-0.10870.06950.04610.0906-0.0430.03090.05790.01860.0673-33.660417.6424-40.7069
53.38641.27710.75752.93331.13237.243-0.09670.2099-0.0518-0.26350.2198-0.12590.11280.2159-0.12320.08570.06310.02180.1716-0.03650.0611-46.284914.3515-5.536
62.47830.88140.72042.33741.50789.43580.1484-0.5573-0.05730.7506-0.1010.0502-0.19830.0976-0.04740.34580.01370.05450.2809-0.0020.162-64.866623.071423.8661
73.2346-4.0727-0.07257.00061.84792.5787-0.1268-0.0039-0.21070.60310.07190.13460.23460.13470.05490.17420.0403-0.02020.05980.05550.0953-53.277312.64268.9417
84.0561-4.0361-0.38278.45431.43422.09530.00960.0448-0.0740.286-0.0322-0.24830.14340.10030.02260.08840.05170.02270.04140.03270.1179-52.00813.01619.7083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 214
2X-RAY DIFFRACTION2B148 - 215
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E147 - 215
6X-RAY DIFFRACTION6F147 - 215
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

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