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- PDB-7mwm: Crystal structure of MBD2 with DNA -

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Basic information

Entry
Database: PDB / ID: 7mwm
TitleCrystal structure of MBD2 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsDNA BINDING PROTEIN/DNA / DNA binding protein-DNA complex / MBD / TAM / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / DNA methylation-dependent heterochromatin formation / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / DNA methylation-dependent heterochromatin formation / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / 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 domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
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: 1.601 Å
AuthorsLiu, K. / Dong, A. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MBD2 with DNA
Authors: Liu, K. / Dong, A. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)32,23641
Polymers32,2366
Non-polymers035
Water5,206289
1
A: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,11820
Polymers16,1183
Non-polymers017
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-5 kcal/mol
Surface area8000 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,11821
Polymers16,1183
Non-polymers018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-5 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.511, 125.435, 40.318
Angle α, β, γ (deg.)90.000, 117.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 8763.156 Da / Num. of mol.: 2 / Fragment: UNP residues 143-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBB5
#2: DNA chain
DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 35 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.79 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96863 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.6→41.81 Å / Num. obs: 86004 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Net I/σ(I): 14.9
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
1.6-1.633.51.085751421370.4460.6781.2831.196.9
8.76-41.813.60.0239482670.9980.0150.02845.294.7

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Processing

Software
NameVersionClassification
REFMAC1.10.1_2155refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C2E

6c2e
PDB Unreleased entry


Resolution: 1.601→31.068 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 2590 3.09 %
Rwork0.186 --
obs0.1867 83814 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.61 Å2 / Biso mean: 25.5719 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 1.601→31.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 976 35 289 2429
Biso mean--31.23 32.56 -
Num. residues----196
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)
11.3932-0.85610.22061.7077-0.02620.8802-0.05890.0565-0.1632-0.05350.0320.12990.0322-0.03610.00050.13670.00420.03140.1304-0.00960.166937.7775-11.2607-0.2246
22.18160.75-0.37761.7322-0.1340.8772-0.0743-0.02990.12520.06460.07330.1563-0.0092-0.05030.00030.124-0.0056-0.02230.1240.00550.140256.38169.36013.632
31.13510.4429-0.68330.7891-0.01630.4672-0.0093-0.1230.07070.06590.17160.0260.37420.38490.00320.20780.03060.03380.2426-0.01520.216351.9613-17.34435.3552
40.09550.50060.34930.59920.3250.4763-0.1438-0.01490.0710.0760.1737-0.10750.47470.11270.00090.2520.01870.01780.23080.03060.212151.5062-18.74355.6302
51.1754-0.38920.70820.66350.370.4569-0.02910.1036-0.012-0.10910.0772-0.0206-0.29590.26850.00920.1654-0.0333-0.02630.19290.01430.140170.487815.5582-2.0934
60.2036-0.599-0.13260.40850.18290.5668-0.1219-0.0066-0.0617-0.16390.1365-0.0459-0.50230.00970.01480.242-0.0243-0.00890.21490.02120.159970.224716.906-2.1277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA142 - 215
2X-RAY DIFFRACTION2chain BB142 - 215
3X-RAY DIFFRACTION3chain CC1 - 12
4X-RAY DIFFRACTION4chain DD1 - 12
5X-RAY DIFFRACTION5chain EE1 - 12
6X-RAY DIFFRACTION6chain FF1 - 12

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