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- PDB-6cnp: Crystal structure of MBD2 complex with methylated CpG island -

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Basic information

Entry
Database: PDB / ID: 6cnp
TitleCrystal structure of MBD2 complex with methylated CpG island
Components
  • DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsTRANSCRIPTION/DNA / 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: 2.1 Å
AuthorsXu, 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: 6C2K
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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 2
B: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,62318
Polymers36,5836
Non-polymers4012
Water61334
1
A: Methyl-CpG-binding domain protein 2
C: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,33111
Polymers18,2913
Non-polymers408
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-13 kcal/mol
Surface area7440 Å2
MethodPISA
2
B: Methyl-CpG-binding domain protein 2
E: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,2917
Polymers18,2913
Non-polymers04
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-5 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.960, 41.320, 58.670
Angle α, β, γ (deg.)101.570, 99.460, 100.540
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: 10934.497 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*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3')


Mass: 3678.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 60.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% PEG550MME, 8% PEG20000, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→39.46 Å / Num. obs: 20704 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 50.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 15.3 / Num. measured all: 80533 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.163.90.9716970.6850.5631.12297.2
8.91-39.463.50.0320.9970.020.03895

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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: pdb entries 2KY8, 3QMG

2ky8

3qmg


Resolution: 2.1→39.457 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.66
Details: Prior to molecular replacement, protein coordinates of the NMR model ensemble of pdb entry 2KY8 were averaged using a program written by Aiping Dong. refmac was used during intermediate ...Details: Prior to molecular replacement, protein coordinates of the NMR model ensemble of pdb entry 2KY8 were averaged using a program written by Aiping Dong. refmac was used during intermediate refinement steps. coot was used for interactive model building. Model geometry was assessed with molprobity.
RfactorNum. reflection% reflection
Rfree0.2177 2109 5.15 %
Rwork0.189 --
obs0.1906 40927 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.94 Å2 / Biso mean: 61.2521 Å2 / Biso min: 33.42 Å2
Refinement stepCycle: final / Resolution: 2.1→39.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 976 12 34 1968
Biso mean--52.69 54.33 -
Num. residues----174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.24771320.27622623275597
2.1489-2.20260.36461230.28282576269997
2.2026-2.26210.31391470.27062576272396
2.2621-2.32870.31151490.26022549269897
2.3287-2.40390.31711160.25692661277797
2.4039-2.48980.32971380.25352600273897
2.4898-2.58940.2611280.25412604273298
2.5894-2.70730.24421020.23412653275597
2.7073-2.84990.34621520.25912591274398
2.8499-3.02840.25891550.23582589274498
3.0284-3.26220.22121680.20612585275397
3.2622-3.59030.20071360.18512411254791
3.5903-4.10930.20891550.16272644279997
4.1093-5.17540.16531360.1442590272698
5.1754-39.46430.18591720.15692566273897
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)
13.1128-0.05950.93013.91670.27071.4034-0.12430.37920.4865-0.9275-0.20150.6459-0.6114-0.26510.22320.43380.03-0.0550.4110.03510.4468-6.985-14.964413.5895
20.8172-1.0945-0.09122.88880.77361.8160.1387-0.71390.17420.886-0.05670.11350.5603-0.3634-0.12030.6498-0.0461-0.0080.5171-0.05590.38528.2251-12.325147.3323
33.1008-0.7214-0.22741.07320.44432.6678-0.0435-0.7379-0.1887-0.13770.12960.014-0.0440.17110.0290.3285-0.0451-0.00830.6060.00740.481-5.8193-30.883215.0722
43.45290.6502-0.4480.70370.48052.2768-0.09720.2274-0.58960.00360.0212-0.03850.09170.02870.10770.3504-0.03410.0030.52630.01960.5702-5.6665-31.380413.7199
52.22451.11370.59224.4768-0.1072.00680.10650.21890.3720.7312-0.646-0.8608-0.2195-0.07730.50330.71620.0072-0.10680.43580.05130.533611.0376-11.081733.3484
62.6358-1.55040.01684.74761.66491.87240.51890.17120.0261-0.4307-0.6190.35910.03420.08450.1570.7163-0.0126-0.02380.4237-0.01740.48949.6715-10.888732.7005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA148 - 215
2X-RAY DIFFRACTION2chain BB153 - 210
3X-RAY DIFFRACTION3chain CC1 - 12
4X-RAY DIFFRACTION4chain DD1 - 12
5X-RAY DIFFRACTION5chain EE1 - 12
6X-RAY DIFFRACTION6chain FF1 - 12

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