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- PDB-6ceu: MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alt... -

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Basic information

Entry
Database: PDB / ID: 6ceu
TitleMBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 3
KeywordsTRANSCRIPTION/DNA / Structural Genomics Consortium / SGC / TRANSCRIPTION-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 / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / FOURIER SYNTHESIS / Resolution: 2.005 Å
AuthorsLiu, K. / Tempel, W. / Wernimont, A.K. / 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 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 3
B: Methyl-CpG-binding domain protein 3
C: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)31,65910
Polymers31,6596
Non-polymers04
Water1,18966
1
A: Methyl-CpG-binding domain protein 3
C: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)15,8305
Polymers15,8303
Non-polymers02
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-6 kcal/mol
Surface area7630 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 3
E: DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)15,8305
Polymers15,8303
Non-polymers02
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-5 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.174, 36.223, 131.157
Angle α, β, γ (deg.)90.000, 92.850, 90.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD3 / Plasmid: PET28-GSTLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95983
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')


Mass: 3662.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 55.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.2M sodium chloride, 0.1M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2→43.69 Å / Num. obs: 23289 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 11.1 / Num. measured all: 84001 / 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
2-2.053.50.826581716790.5720.5110.9741.598.7
8.94-43.693.20.0339162860.9970.0210.03927.396.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: early version of model from PDB entry 6CC8

6cc8


Resolution: 2.005→35.202 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78
Details: Electron density did not permit unambiguous distinction between strands of non-palindromic DNA. refmac was used for intermediate refinement steps. coot was used for interactive model ...Details: Electron density did not permit unambiguous distinction between strands of non-palindromic DNA. refmac was used for intermediate refinement steps. coot was used for interactive model building. Model geometry was validated with molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1312 5.72 %thinshells (sftools)
Rwork0.2145 ---
obs0.2167 22928 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.22 Å2 / Biso mean: 43.1122 Å2 / Biso min: 24.87 Å2
Refinement stepCycle: final / Resolution: 2.005→35.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 976 4 66 2146
Biso mean--40.63 41.36 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072224
X-RAY DIFFRACTIONf_angle_d1.1013203
X-RAY DIFFRACTIONf_chiral_restr0.064330
X-RAY DIFFRACTIONf_plane_restr0.007247
X-RAY DIFFRACTIONf_dihedral_angle_d26.8141142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0053-2.08560.32331530.27182294244799
2.0856-2.18050.3141820.269223572539100
2.1805-2.29540.30771320.254924002532100
2.2954-2.43920.31551130.247324582571100
2.4392-2.62750.29431340.25824132547100
2.6275-2.89180.28211520.271224292581100
2.8918-3.310.28461620.23892384254699
3.31-4.16920.21511400.18532364250498
4.1692-35.20690.20891440.17362517266199
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)
12.55480.10890.50772.8322-3.52428.22390.1246-0.157-0.1096-0.0061-0.01520.04850.2101-0.2799-0.11780.40530.0274-0.02660.3236-0.01240.2809-23.7783-4.546855.2502
22.9298-0.669-1.20323.294-3.75315.63890.11220.2250.072-0.0354-0.07510.0213-0.2697-0.3142-0.04870.4314-0.03120.00360.2972-0.01710.2324-20.78966.509610.1363
35.9913-3.86321.50484.4982-0.21772.3439-0.1110.18640.2419-0.0777-0.0603-0.1566-0.16470.14240.21720.31960.06060.0140.3441-0.01840.3713-19.42628.270346.2634
41.04930.5625-0.57981.45561.17752.23330.12430.55380.21130.0529-0.08650.0192-0.18430.3157-0.08220.28940.1320.03150.4402-0.02280.3936-19.63677.73845.0069
56.30593.1217-1.61222.73130.00982.8117-0.0587-0.4915-0.2184-0.107-0.0524-0.16610.05860.20510.14270.3405-0.022-0.04390.2869-0.01120.3875-16.3508-6.259919.2217
62.18450.16470.91641.93840.71422.35860.0539-0.89960.0541-0.1877-0.1958-0.0985-0.2170.49970.06440.3701-0.1215-0.04720.4206-0.0540.3402-16.5755-5.684720.5195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 71
2X-RAY DIFFRACTION2chain BB1 - 71
3X-RAY DIFFRACTION3chain CC1 - 12
4X-RAY DIFFRACTION4chain DD1 - 12
5X-RAY DIFFRACTION5chain EE1 - 12
6X-RAY DIFFRACTION6chain FF1 - 12

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