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- PDB-3vyq: Crystal structure of the methyl CpG Binding Domain of MBD4 in com... -

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Basic information

Entry
Database: PDB / ID: 3vyq
TitleCrystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
Components
  • DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3')
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / methyl CpG binding domain / protein-DNA complex / versatile base recognition / HYDROLASE-DNA complex
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin ...Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm
Similarity search - Function
Methyl-CpG-binding domain protein 4 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / DNA glycosylase / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily ...Methyl-CpG-binding domain protein 4 / Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / DNA glycosylase / 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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.525 Å
AuthorsOtani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Ariyoshi, M. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4
Authors: Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Kimura, H. / Suetake, I. / Tajima, S. / Ariyoshi, M. / Shirakawa, M.
History
DepositionOct 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 4
B: DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3')
C: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3')
D: Methyl-CpG-binding domain protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6608
Polymers23,4024
Non-polymers2584
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-60 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.604, 34.093, 61.165
Angle α, β, γ (deg.)75.28, 77.76, 87.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )
21chain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLNGLNchain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )AA71 - 839 - 21
12LEULEUGLYGLYchain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )AA85 - 8723 - 25
13PHEPHEPHEPHEchain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )AA97 - 10535 - 43
14SERSERLEULEUchain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )AA110 - 11648 - 54
15ASNASNVALVALchain A and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )AA118 - 13256 - 70
21LYSLYSGLNGLNchain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )DD71 - 839 - 21
22LEULEUGLYGLYchain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )DD85 - 8723 - 25
23PHEPHEPHEPHEchain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )DD97 - 10535 - 43
24SERSERLEULEUchain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )DD110 - 11648 - 54
25ASNASNVALVALchain D and (resseq 71:83 or resseq 85:87 or resseq 97:105 or resseq 110:116 or resseq 118:132 )DD118 - 13256 - 70

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Methyl-CpG-binding domain protein 4 / Methyl-CpG-binding protein MBD4 / Mismatch-specific DNA N-glycosylase


Mass: 8332.593 Da / Num. of mol.: 2 / Fragment: methyl CpG binding domain, UNP residues 63-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbd4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z2D7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3')


Mass: 3372.238 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3')


Mass: 3364.208 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 59 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2mM zinc acetate, 100mM sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 7786 / Num. obs: 7225 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 35.89 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.4 / % possible all: 67.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VXV

3vxv


Resolution: 2.525→32.972 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 0.07 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 323 4.55 %RANDOM
Rwork0.1934 ---
obs0.1954 7095 90.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.543 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 109.83 Å2 / Biso mean: 36.5379 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1--4.2347 Å2-8.443 Å2-4.6272 Å2
2--5.9693 Å22.7744 Å2
3----1.7345 Å2
Refinement stepCycle: LAST / Resolution: 2.525→32.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 429 7 55 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071542
X-RAY DIFFRACTIONf_angle_d1.1612158
X-RAY DIFFRACTIONf_dihedral_angle_d23.241605
X-RAY DIFFRACTIONf_chiral_restr0.062228
X-RAY DIFFRACTIONf_plane_restr0.004201
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A376X-RAY DIFFRACTIONPOSITIONAL0.037
12D376X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5253-3.18120.33471490.2485309382
3.1812-32.97520.20571740.1745367998
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)
13.0406-0.43560.56840.935-0.29842.1090.2038-0.5951-0.0653-0.06620.08450.1188-0.0179-0.0396-0.15960.13820.02860.0360.29430.00250.073513.0063-10.40659.1365
24.709-4.02053.85157.7506-3.17375.46140.27640.39290.6010.141-0.8930.1245-0.91290.3172-0.24170.32940.08260.01760.136-0.05880.212211.581-8.714-5.848
32.5678-0.5116-0.95720.5355-0.81782.81190.2461-0.024-0.0368-0.3666-0.4822-0.021-0.1797-0.24250.15510.32760.0295-0.03160.12570.0060.154411.8095-10.514-5.3296
42.2885-0.09770.45551.0114-0.11881.079-0.13580.0607-0.32820.05220.2831-0.0335-0.05550.0083-0.10950.1750.12290.06390.41760.02620.082910.3282-26.2174-22.2785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 70:132)A70 - 132
2X-RAY DIFFRACTION2(chain B and resid 2:11)B2 - 11
3X-RAY DIFFRACTION3(chain C and resid 1:11)C1 - 11
4X-RAY DIFFRACTION4(chain D and resid 70:132)D70 - 132

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