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- PDB-6c1a: MBD2 in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 6c1a
TitleMBD2 in complex with methylated DNA
Components
  • Methyl-CpG-binding domain protein 2
  • complement to dna strand 1
  • dna strand 1DNA
KeywordsDNA BINDING PROTEIN/DNA / dna methylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLiu, K. / Xu, C. / 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 4, 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
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: dna strand 1
D: complement to dna strand 1
E: Methyl-CpG-binding domain protein 2
F: Methyl-CpG-binding domain protein 2
G: dna strand 1
H: complement to dna strand 1


Theoretical massNumber of molelcules
Total (without water)49,84460
Polymers49,8448
Non-polymers052
Water2,072115
1
A: Methyl-CpG-binding domain protein 2
B: Methyl-CpG-binding domain protein 2
C: dna strand 1
D: complement to dna strand 1


Theoretical massNumber of molelcules
Total (without water)24,92233
Polymers24,9224
Non-polymers029
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Methyl-CpG-binding domain protein 2
F: Methyl-CpG-binding domain protein 2
G: dna strand 1
H: complement to dna strand 1


Theoretical massNumber of molelcules
Total (without water)24,92227
Polymers24,9224
Non-polymers023
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.533, 39.875, 105.151
Angle α, β, γ (deg.)83.970, 85.700, 62.750
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-pRARE2 / References: UniProt: Q9UBB5
#2: DNA chain dna strand 1 / DNA


Mass: 3727.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#3: DNA chain complement to dna strand 1


Mass: 3612.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 52 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→35.34 Å / Num. obs: 31675 / % possible obs: 96.2 % / Redundancy: 2.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.06 / Rrim(I) all: 0.09 / Net I/σ(I): 9.6 / Num. measured all: 69361 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.110.663552425200.4950.5970.8951.496.8
8.94-35.340.0228033660.9980.020.0330.492

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: currently unpublished model

Resolution: 2.05→34.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.006 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Arp/warp was used in atom update/map improvement mode. coot was used for interactive model building. Model geometry was assessed with molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1224 3.9 %thin shells (sftools)
Rwork0.2305 ---
obs0.2319 30448 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.68 Å2 / Biso mean: 36.197 Å2 / Biso min: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.02 Å20.2 Å2
2---0.71 Å20.11 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 2.05→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 974 52 115 3178
Biso mean--29.49 29.27 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0173209
X-RAY DIFFRACTIONr_bond_other_d0.0030.022468
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.74528
X-RAY DIFFRACTIONr_angle_other_deg1.13835719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.57321.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.721522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
X-RAY DIFFRACTIONr_mcbond_it1.0452.1251080
X-RAY DIFFRACTIONr_mcbond_other1.0392.1211077
X-RAY DIFFRACTIONr_mcangle_it1.6883.1751346
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 150 -
Rwork0.32 2264 -
all-2414 -
obs--96.83 %
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)
13.5253-1.2335-2.13662.04271.27116.39020.0127-0.23350.08160.19740.046-0.2068-0.10510.0746-0.05870.0708-0.0634-0.01150.1341-0.02850.0283-27.691215.6961-25.5338
24.5743-0.145-3.91661.6712-0.14477.7937-0.02110.9185-0.165-0.602-0.19980.16870.0811-0.46770.22090.2480.03-0.04940.2556-0.05310.028-44.82036.9078-54.5318
34.07343.78720.07367.76920.61011.2114-0.04730.02710.0947-0.377-0.0408-0.0945-0.15960.06430.08810.0583-0.03480.00480.05840.00580.0209-34.581316.3692-39.8828
43.72343.33930.15217.89410.6951.94740.0555-0.0730.0054-0.1495-0.008-0.4561-0.11080.1873-0.04750.0351-0.02370.01430.0505-0.0030.0442-33.163516.4958-40.7212
52.57530.95951.50212.05130.91546.08-0.03140.1302-0.0839-0.17670.054-0.14630.10920.106-0.02260.08770.08710.00150.1756-0.0370.0185-45.95714.6354-5.4009
63.69810.49011.08262.8069-0.85016.45780.0733-0.75150.07840.8776-0.20810.0596-0.2859-0.01120.13480.31240.01050.00880.2711-0.03080.0081-63.499223.736523.8576
73.1538-4.0276-0.29297.57850.63061.7035-0.0828-0.0088-0.12760.4425-0.009-0.07960.15310.05310.09180.0820.0482-0.0190.08740.01330.0367-52.783913.98369.1459
84.4284-3.7394-0.56927.36191.10521.83680.06610.054-0.0590.0988-0.0286-0.41920.08510.1346-0.03740.05710.0458-0.01080.07920.01730.0589-51.359113.90839.9527
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 DIFFRACTION5E148 - 215
6X-RAY DIFFRACTION6F148 - 215
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

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