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- PDB-6c1v: MBD2 in complex with double-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 6c1v
TitleMBD2 in complex with double-stranded DNA
Components
  • (12-mer DNA) x 2
  • Methyl-CpG-binding domain protein 2
KeywordsDNA BINDING PROTEIN/DNA / MBD / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding ...satellite DNA binding / NuRD complex / DNA methylation-dependent heterochromatin formation / methyl-CpG binding / C2H2 zinc finger domain binding / RNA Polymerase I Promoter Opening / NoRC negatively regulates rRNA expression / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / 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 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsLei, M. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.
Authors: Liu, K. / Xu, C. / Lei, M. / Yang, A. / Loppnau, P. / Hughes, T.R. / Min, J.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / 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 / _citation_author.name
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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: 12-mer DNA
D: 12-mer DNA
E: Methyl-CpG-binding domain protein 2
F: Methyl-CpG-binding domain protein 2
G: 12-mer DNA
H: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,08944
Polymers49,8188
Non-polymers277,27136
Water52229
1
A: Methyl-CpG-binding domain protein 2
B: Methyl-CpG-binding domain protein 2
C: 12-mer DNA
D: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,94924
Polymers24,9094
Non-polymers154,03920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Methyl-CpG-binding domain protein 2
F: Methyl-CpG-binding domain protein 2
G: 12-mer DNA
H: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,14120
Polymers24,9094
Non-polymers123,23216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.013, 40.198, 105.158
Angle α, β, γ (deg.)84.500, 85.480, 62.710
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 8791.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-RIL / References: UniProt: Q9UBB5
#2: DNA chain 12-mer DNA


Mass: 3743.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 12-mer DNA


Mass: 3583.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 7701.970 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.9 Å3/Da / Density % sol: 57.66 % / Mosaicity: 0.24 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG-3350, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→35.64 Å / Num. obs: 34483 / % possible obs: 94.8 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.037 / Rrim(I) all: 0.054 / Net I/σ(I): 10 / Num. measured all: 66586 / Scaling rejects: 0
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
2-2.051.70.76366621990.4650.6941.0320.981.4
8.93-35.641.90.0247693960.9980.0210.03131.396.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.

Resolution: 2.3→34.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.487 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2677 821 3.6 %
Rwork0.2327 --
obs0.234 22079 96.09 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.62 Å2 / Biso mean: 49.143 Å2 / Biso min: 21.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å2-0.48 Å20.31 Å2
2--0.58 Å20.04 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 2.3→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 972 36 29 3061
Biso mean--36.87 34.54 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0163162
X-RAY DIFFRACTIONr_bond_other_d0.0020.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6724462
X-RAY DIFFRACTIONr_angle_other_deg1.2335554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65921.28278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43915329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1081519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02717
X-RAY DIFFRACTIONr_mcbond_it1.3652.9031078
X-RAY DIFFRACTIONr_mcbond_other1.3572.8991075
X-RAY DIFFRACTIONr_mcangle_it2.1614.3431342
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.11 1 -
Rwork0.292 1738 -
all-1739 -
obs--96.56 %
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)
12.7819-1.7094-0.27813.28491.84016.4315-0.0185-0.30480.04010.35430.1616-0.2959-0.17840.3234-0.14310.1832-0.08350.01520.2958-0.05330.0977-28.033116.3941-25.184
23.904-0.8871-3.8412.2721-0.9787.69430.1010.7029-0.0053-0.744-0.11990.19250.0388-0.57850.01880.4152-0.0685-0.06460.3319-0.04490.0756-45.75427.4734-54.538
34.06964.40980.17377.51362.00752.6519-0.1137-0.00130.2188-0.50630.1228-0.0491-0.21060.0013-0.00910.0836-0.03380.03270.1073-0.00350.0666-34.988117.1824-39.778
45.31945.03390.14829.5891.09332.23560.1684-0.17360.1191-0.0537-0.1472-0.4886-0.1193-0.0143-0.02120.1151-0.03260.00730.06350.01980.0945-33.692517.0309-40.5977
53.22222.09491.37413.51511.50816.3837-0.07390.407-0.0841-0.36080.2242-0.28320.16130.2632-0.15030.14830.13110.01290.2663-0.04780.1194-46.67914.7521-5.5113
62.93750.28680.8092.9904-0.78616.63680.1079-0.6228-0.03160.8571-0.13340.0681-0.1685-0.22870.02550.3260.02640.03690.2338-0.02650.0646-64.641623.519623.9552
74.2394-4.244-0.47576.69273.23843.5131-0.1434-0.0033-0.22340.63030.20670.06630.35170.1291-0.06330.22930.1058-0.05770.07080.00410.0905-53.320213.769.0937
85.1224-4.5310.37558.61260.13762.0870.21140.2075-0.2120.0508-0.1743-0.36750.1930.0249-0.0370.11140.06050.01510.04160.02140.1129-52.10813.98559.8699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A148 - 215
2X-RAY DIFFRACTION2B147 - 214
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E148 - 215
6X-RAY DIFFRACTION6F148 - 215
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

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