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- PDB-6cc8: Crystal structure MBD3 MBD domain in complex with methylated CpG DNA -

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Basic information

Entry
Database: PDB / ID: 6cc8
TitleCrystal structure MBD3 MBD domain in complex with methylated CpG DNA
Components
  • Methyl-CpG-binding domain protein 3
  • methylated CpG DNA
KeywordsDNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 ...ventricular cardiac muscle tissue development / NuRD complex / regulation of cell fate specification / regulation of stem cell differentiation / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / RNA Polymerase I Transcription Initiation / embryonic organ development / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / response to nutrient levels / response to estradiol / in utero embryonic development / Potential therapeutics for SARS / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLiu, K. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Febs J. / Year: 2019
Title: Structural analyses reveal that MBD3 is a methylated CG binder.
Authors: Liu, K. / Lei, M. / Wu, Z. / Gan, B. / Cheng, H. / Li, Y. / Min, J.
History
DepositionFeb 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_asym
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id
Revision 2.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 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 3
B: Methyl-CpG-binding domain protein 3
C: methylated CpG DNA
D: methylated CpG DNA
E: methylated CpG DNA
F: methylated CpG DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,89518
Polymers31,6576
Non-polymers1,23712
Water1,15364
1
A: Methyl-CpG-binding domain protein 3
C: methylated CpG DNA
D: methylated CpG DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3448
Polymers15,8293
Non-polymers5165
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-2 kcal/mol
Surface area7610 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 3
E: methylated CpG DNA
F: methylated CpG DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,55010
Polymers15,8293
Non-polymers7227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-3 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.550, 36.640, 130.930
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-CpG-binding domain protein 3 / Methyl-CpG-binding protein MBD3


Mass: 8473.716 Da / Num. of mol.: 2 / Fragment: MBD domain (UNP residues 1-71)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD3 / Plasmid: pET28-GSTLIC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95983
#2: DNA chain
methylated CpG DNA


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


Mass: 103.120 Da / Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 55.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.95→35.73 Å / Num. obs: 25160 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.761 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6C2K

6c2k
PDB Unreleased entry


Resolution: 1.95→35.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.689 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156
Details: MODEL WAS ORIGINALLY REFINED AGAINST DATA COLLECTED ON AN ISOMORPHOUS CRYSTAL. THAT STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND MOLREP TO POSITION FIRST AND SECOND COPY OF ...Details: MODEL WAS ORIGINALLY REFINED AGAINST DATA COLLECTED ON AN ISOMORPHOUS CRYSTAL. THAT STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND MOLREP TO POSITION FIRST AND SECOND COPY OF THE COMPLEX, RESPECTIVELY. REFMAC WAS USED DURING INTERMEDIATE REFINEMENT. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ASSESSED ON THE MOLPROBITY SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1436 5.7 %THIN RESOLUTION SHELLS (SFTOOLS)
Rwork0.224 ---
obs0.226 23724 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20.06 Å2
2--0.8 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 976 12 64 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0162258
X-RAY DIFFRACTIONr_bond_other_d0.0030.021614
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.6173247
X-RAY DIFFRACTIONr_angle_other_deg1.2633743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.40519.41251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06215197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.331517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211865
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02512
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7832.368570
X-RAY DIFFRACTIONr_mcbond_other1.7832.364569
X-RAY DIFFRACTIONr_mcangle_it2.7693.527710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 104 -
Rwork0.312 1775 -
obs--99.52 %
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)
12.47440.302-0.73923.5152-2.00894.48110.0083-0.1273-0.17770.13440.05270.0710.2197-0.3109-0.0610.21420.01070.01350.17820.00020.021-23.4294-4.708554.8601
22.7592-0.60270.63833.1747-1.76754.37920.04610.12260.2067-0.18060.06950.0699-0.231-0.1989-0.11550.192-0.02240.02850.143400.0274-20.30976.796710.3602
33.9286-3.6834-0.29934.5481-0.32191.61460.0020.04960.3829-0.1249-0.0613-0.1461-0.00810.00140.05930.19220.05490.04350.22580.00910.1501-18.88258.227646.485
46.2491-1.51071.46512.44220.36521.72770.01550.29510.3455-0.0277-0.1512-0.1632-0.01890.00870.13570.17410.06920.0970.21590.01790.1161-18.81077.369545.1612
53.86993.25120.40734.1274-0.59992.0485-0.0562-0.0091-0.43050.002-0.0204-0.1255-0.00890.02760.07660.1166-0.0667-0.0040.1827-0.0130.1574-15.9889-6.141218.9401
66.12522.1094-1.27383.2210.03941.75770.1021-0.3004-0.28970.0558-0.1164-0.08680.05640.06170.01440.1267-0.06-0.06370.1970.00690.13-15.8663-5.308820.2656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION2B1 - 71
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12

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