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- PDB-7kz1: Human MBD4 glycosylase domain bound to DNA containing an abasic site -

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Basic information

Entry
Database: PDB / ID: 7kz1
TitleHuman MBD4 glycosylase domain bound to DNA containing an abasic site
Components
  • DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol ...satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol / nuclear speck / DNA repair / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Methyl-CpG-binding domain protein 4 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsPidugu, L.S. / Bright, H. / Pozharski, E. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM072711, R35-GM136225 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Mechanism of Base Excision by MBD4.
Authors: Pidugu, L.S. / Bright, H. / Lin, W.J. / Majumdar, C. / Van Ostrand, R.P. / David, S.S. / Pozharski, E. / Drohat, A.C.
History
DepositionDec 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0846
Polymers25,9073
Non-polymers1773
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-24 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.669, 54.292, 98.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18671.521 Da / Num. of mol.: 1 / Fragment: glycosylase domain (UNP residues 426-580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*CP*GP*(ORP)P*GP*CP*AP*GP*C)-3')


Mass: 3540.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')


Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 155 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG400, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.62→37.61 Å / Num. obs: 28461 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.996 / Rpim(I) all: 0.058 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.62-1.651213610.2391.537198.3
8.88-37.6111.52220.9980.023199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DK9

4dk9


Resolution: 1.62→37.61 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1376 4.88 %
Rwork0.1818 26830 -
obs0.1829 28206 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.52 Å2 / Biso mean: 37.2099 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 1.62→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 479 11 158 1839
Biso mean--61 45.96 -
Num. residues----167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.680.34331240.31962488261294
1.68-1.750.32451230.292626622785100
1.75-1.830.25911400.252526512791100
1.83-1.920.28561390.226826572796100
1.92-2.040.23531290.206926732802100
2.04-2.20.23581420.187126652807100
2.2-2.420.22721460.181426952841100
2.42-2.770.20971450.181527022847100
2.77-3.490.20331330.165927572890100
3.49-37.610.15831550.154828803035100
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)
14.4561-1.1495-3.08343.4833-1.64443.9836-0.0567-0.3948-0.6084-0.0226-0.1168-0.23250.43610.6040.02940.17610.0524-0.02290.28090.04910.2966-5.2846-16.403817.3377
22.74850.7224-0.24233.15970.18542.18230.1364-0.24130.22190.3046-0.13880.1241-0.1276-0.07340.01020.1415-0.00610.00710.1463-0.03520.1085-18.8529-1.65620.7562
35.46530.2404-2.00657.37191.15642.46830.11080.5329-0.2805-0.2099-0.15080.52880.1473-0.43810.02540.22380.0156-0.04550.2349-0.06060.2026-21.5791-10.31286.9859
46.0953-0.9677-2.36254.3614-1.67424.79210.12810.2728-0.2645-0.4707-0.1416-0.01890.16970.0187-0.00810.19090.02-0.0250.1953-0.04980.119-8.602-12.74976.108
57.2456-4.0739-0.84293.84083.45498.09330.1111-0.24710.0624-0.59710.2385-0.90310.0250.7205-0.37470.17310.01790.04190.3471-0.01140.30611.7248-12.60238.2031
66.3488-0.7978-4.2242.3546-1.42226.9454-0.59390.4036-2.5094-0.1949-0.80680.52291.54060.92611.57290.55520.1712-0.24990.5067-0.24220.7802-2.0534-22.289211.4891
70.25940.5974-0.1692.99542.27254.7808-0.57240.35050.8903-0.84880.5193-0.4933-0.89180.44740.2190.3424-0.0246-0.09630.2389-0.00190.6179-9.025910.042511.5577
88.25581.60151.67872.8354-1.39214.8128-0.1990.24610.1258-0.60090.2325-0.6513-0.39090.4339-0.11320.3948-0.05390.05430.1876-0.11150.514-7.722311.821613.7187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 436 through 455 )A436 - 455
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 525 )A456 - 525
3X-RAY DIFFRACTION3chain 'A' and (resid 526 through 538 )A526 - 538
4X-RAY DIFFRACTION4chain 'A' and (resid 539 through 560 )A539 - 560
5X-RAY DIFFRACTION5chain 'A' and (resid 561 through 573 )A561 - 573
6X-RAY DIFFRACTION6chain 'A' and (resid 574 through 580 )A574 - 580
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 12 )C1 - 12
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 12 )D1 - 12

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