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- PDB-5w9q: Zinc finger region of MBD1 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 5w9q
TitleZinc finger region of MBD1 in complex with CpG DNA
Components
  • Methyl-CpG-binding domain protein 1
  • dna
KeywordsDNA BINDING PROTEIN/DNA / zinc finger / dna-binding / CXXC3 / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / negative regulation of astrocyte differentiation / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation ...double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / negative regulation of astrocyte differentiation / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation / nuclear matrix / response to estradiol / transcription by RNA polymerase II / nuclear speck / response to xenobiotic stimulus / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: 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 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 1
B: Methyl-CpG-binding domain protein 1
C: dna
D: dna
E: dna
F: dna
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,92226
Polymers28,6606
Non-polymers26220
Water82946
1
A: Methyl-CpG-binding domain protein 1
C: dna
D: dna
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,46113
Polymers14,3303
Non-polymers13110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-13 kcal/mol
Surface area7020 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 1
E: dna
F: dna
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,46113
Polymers14,3303
Non-polymers13110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-14 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.339, 27.800, 64.914
Angle α, β, γ (deg.)90.000, 106.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-CpG-binding domain protein 1 / CXXC-type zinc finger protein 3 / Methyl-CpG-binding protein MBD1 / Protein containing methyl-CpG- ...CXXC-type zinc finger protein 3 / Methyl-CpG-binding protein MBD1 / Protein containing methyl-CpG-binding domain 1


Mass: 7003.344 Da / Num. of mol.: 2 / Fragment: Zinc finger region (UNP residues 330-388)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD1, CXXC3, PCM1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9UIS9
#2: DNA chain
dna


Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 16 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.8→33.69 Å / Num. obs: 22639 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 13.3 / Num. measured all: 83217 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.843.70.726495713370.8070.4350.8481.999.9
9-33.693.10.0426162010.9950.0290.05130.797.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4HP3, 3QMD

4hp3

3qmd


Resolution: 1.8→33.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.831 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.139
Details: arp/warp was used in map improvement mode. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1306 5.8 %thin shells (sftools)
Rwork0.2262 ---
obs0.2277 21331 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 48.642 Å2 / Biso min: 25.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20.36 Å2
2---4.31 Å2-0 Å2
3---4.86 Å2
Refinement stepCycle: final / Resolution: 1.8→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 972 20 46 1877
Biso mean--45.2 40.91 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0151976
X-RAY DIFFRACTIONr_bond_other_d0.0040.021370
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.4972843
X-RAY DIFFRACTIONr_angle_other_deg1.3673.013163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85519.76242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4681518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021564
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
X-RAY DIFFRACTIONr_mcbond_it0.8361.341441
X-RAY DIFFRACTIONr_mcbond_other0.8151.339440
X-RAY DIFFRACTIONr_mcangle_it1.3931.996547
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 69 -
Rwork0.362 1610 -
all-1679 -
obs--99.82 %
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)
111.40050.51151.851310.18982.40655.26090.20280.8672-0.1789-0.3113-0.08290.1841-0.0320.4125-0.11990.2670.009-0.02150.3848-0.02550.0111-11.975611.96378.0522
211.8033-5.53432.839111.0574-0.09545.7105-0.1567-0.9859-0.18680.7590.1650.28680.1163-0.4832-0.00830.3228-0.0006-0.02650.3971-0.04280.0723-22.84936.1379-8.3201
311.02232.2064-2.55684.5220.06392.61710.1601-0.9795-0.12290.3568-0.2859-0.0795-0.07740.19980.12580.3431-0.0528-0.06860.4207-0.01530.0836-10.96499.214321.6868
412.74187.2853-1.543810.1215-0.6912.7607-0.0166-0.1545-0.92990.24640.0346-0.3539-0.20360.1161-0.01790.4144-0.0345-0.01170.3798-0.02870.0877-10.72758.059920.298
58.5686-4.2305-1.53255.0978-0.35211.23460.40190.8027-0.2986-0.4818-0.52270.4273-0.065-0.06530.12080.35270.0664-0.15170.4462-0.0610.2604-23.77752.3751-22.1177
613.2381-8.7748-0.09447.3589-0.17612.03110.20570.4045-1.0322-0.255-0.25590.6211-0.0839-0.19360.05010.40670.0472-0.06210.4296-0.03790.242-23.8871.3871-20.8795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A333 - 1002
2X-RAY DIFFRACTION2B334 - 1002
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12

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