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- PDB-6cnq: MBD2 in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 6cnq
TitleMBD2 in complex with methylated DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsTRANSCRIPTION/DNA / dna methylation / dna binding / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-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 / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsLiu, K. / Xu, C. / 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
DepositionMar 8, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2018ID: 6C2E
Revision 1.0Mar 28, 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
Revision 1.2May 23, 2018Group: 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 2
B: Methyl-CpG-binding domain protein 2
D: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)32,29210
Polymers32,2926
Non-polymers04
Water52229
1
A: Methyl-CpG-binding domain protein 2
D: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1463
Polymers16,1463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-4 kcal/mol
Surface area7340 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1467
Polymers16,1463
Non-polymers04
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-5 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 40.500, 202.896
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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.: 2 / Fragment: 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) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9UBB5
#2: DNA chain
DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)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 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→40.58 Å / Num. obs: 20266 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Net I/σ(I): 18.1 / Num. measured all: 114295 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.225.80.86417320.7710.3970.951100
8.87-40.5850.0240.9980.0120.02791

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: earlier version of PDB entry 6C2K, unpublished DNA model

6c2k
PDB Unreleased entry


Resolution: 2.151→24.344 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.05
Details: arp/warp was used in map improvement mode. refmac was used at intermediate stages of refinement. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1398 3.47 %thin shells (sftools)
Rwork0.2057 ---
obs0.2065 40238 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.47 Å2 / Biso mean: 63.028 Å2 / Biso min: 35.57 Å2
Refinement stepCycle: final / Resolution: 2.151→24.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 976 4 29 2048
Biso mean--55.88 50.34 -
Num. residues----184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1508-2.22760.3282720.329437504022100
2.2276-2.3168100000000.31344028100
2.3168-2.42210.28412320.294538604092100
2.4221-2.5497100000000.2874078100
2.5497-2.70920.33482000.285938484048100
2.7092-2.91810.39461960.30338304026100
2.9181-3.21120.32021400.275238333973100
3.2112-3.67450.2943840.20733934401898
3.6745-4.62420.1541400.16238433983100
4.6242-24.34570.131340.13523836397098
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)
10.54510.49960.58911.0680.73241.95030.1123-0.0709-0.248-0.02340.0610.28260.4679-0.8633-0.01190.86840.0297-0.01820.56760.05120.447834.75720.5638-4.7351
21.01410.49450.66680.75280.97212.58160.1626-0.2655-0.63750.4777-0.33030.23120.6695-1.0871-0.07340.73720.0614-0.03940.79260.03280.575728.392510.409-30.4128
31.0429-0.27020.58930.10310.01080.73030.33730.54930.2508-0.1771-0.6659-0.63120.15790.3782-0.00350.97530.0594-0.00930.53010.06290.642148.668826.05761.0116
40.2450.2302-0.18920.2651-0.07850.5506-0.28610.30570.15181.1158-0.1247-0.5344-0.07960.2199-0.00680.97520.0591-0.07110.58720.02850.660948.478426.07991.898
50.84620.88190.39141.5871-0.06390.94640.96540.87090.5999-0.2882-1.4686-0.4951-0.20760.1737-0.89650.73610.5868-0.01550.64290.01970.732639.572819.7541-37.5497
60.9480.50770.05030.2658-0.28471.5297-0.487-0.01440.16051.05870.1951-0.481-0.1932-0.0521-0.36450.70190.328-0.12870.51470.01860.625739.70820.2761-35.9768
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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