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

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Basic information

Entry
Database: PDB / ID: 7mwk
TitleCrystal structure of MBD2 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(MC)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 / siRNA binding / maternal behavior / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / positive regulation of Wnt signaling pathway / embryonic organ development ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / siRNA binding / maternal behavior / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / positive regulation of Wnt signaling pathway / embryonic organ development / response to mechanical stimulus / heterochromatin / 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: 2.453 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)32,23610
Polymers32,2366
Non-polymers04
Water905
1
A: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1183
Polymers16,1183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-6 kcal/mol
Surface area7460 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(MC)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1187
Polymers16,1183
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-5 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.521, 40.521, 202.097
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain F
21chain C
31chain D
41chain E
12(chain A and (resseq 148:159 or (resid 160 and (name...
22(chain B and (resseq 148:175 or (resid 176 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DGDGDCDCchain FFF1 - 121 - 12
211DGDGDCDCchain CCC1 - 121 - 12
311DGDGDCDCchain DDD1 - 121 - 12
411DGDGDCDCchain EEE1 - 121 - 12
112LYSLYSTRPTRP(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 1597 - 18
122LYSLYSLYSLYS(chain A and (resseq 148:159 or (resid 160 and (name...AA16019
132LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
142LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
152LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
162LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
172LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
182LYSLYSPROPRO(chain A and (resseq 148:159 or (resid 160 and (name...AA148 - 2157 - 74
212LYSLYSSERSER(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 1757 - 34
222ASPASPASPASP(chain B and (resseq 148:175 or (resid 176 and (name...BB17635
232LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
242LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
252LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
262LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74
272LYSLYSPROPRO(chain B and (resseq 148:175 or (resid 176 and (name...BB148 - 2157 - 74

NCS ensembles :
ID
1
2

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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*AP*(MC)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.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.97 Å3/Da / Density % sol: 58.61 % / Mosaicity: 0.18 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→34.575 Å / Num. obs: 27350 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 61.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Net I/σ(I): 18.9
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
2.45-2.555.81.063919115780.5750.481.1671.8100
8.83-34.575.30.02615482930.9990.0120.02954.197.9

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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: 2.453→34.575 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 890 3.31 %
Rwork0.1915 --
obs0.1924 26856 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.9 Å2 / Biso mean: 63.2246 Å2 / Biso min: 38.04 Å2
Refinement stepCycle: final / Resolution: 2.453→34.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 976 4 5 2019
Biso mean--44.78 52.31 -
Num. residues----184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11F412X-RAY DIFFRACTION6.977TORSIONAL
12C412X-RAY DIFFRACTION6.977TORSIONAL
13D412X-RAY DIFFRACTION6.977TORSIONAL
14E412X-RAY DIFFRACTION6.977TORSIONAL
21A594X-RAY DIFFRACTION6.977TORSIONAL
22B594X-RAY DIFFRACTION6.977TORSIONAL
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)
10.4284-0.41530.53711.51770.44781.03340.0922-0.0593-0.08760.0714-0.02360.29980.2027-0.3519-00.8336-0.02540.07660.47290.00530.383434.967720.8244-4.9456
21.0730.57490.01451.1244-0.73730.66190.3264-0.0201-0.21070.2133-0.33930.2042-0.0853-0.4786-0.01330.6570.0864-0.06190.5414-0.02950.451628.622810.2673-30.2582
30.1042-1.27810.3835-0.0424-0.25610.80580.16420.28440.1448-0.1952-0.2547-0.2011-0.01090.202401.01550.00070.10730.53250.01170.654249.037926.09710.9721
4-0.2410.0804-0.74120.4669-0.23060.8253-0.25950.32940.21670.6194-0.1057-0.3454-0.02780.059601.02230.01850.02240.51660.04280.594848.600126.04682.4765
51.53090.60340.83680.27440.3820.60380.50010.35330.2609-0.2044-0.7437-0.25790.11520.156-0.06660.80140.3971-0.01940.5635-0.0390.670739.919819.8663-37.4415
60.06940.8127-0.56340.8396-0.81881.6838-0.08230.17420.2550.34-0.2885-0.2796-0.09330.01860.00040.71180.2696-0.1430.4915-0.06710.667539.916820.397-35.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA148 - 215
2X-RAY DIFFRACTION2chain BB148 - 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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