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- PDB-7kz0: Human MBD4 glycosylase domain bound to DNA containing substrate a... -

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Basic information

Entry
Database: PDB / ID: 7kz0
TitleHuman MBD4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine
Components
  • DNA (5'-D(*CP*CP*AP*GP*CP*GP*(P2U)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 / MBD4 / 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 / Resolution: 1.57 Å
AuthorsPidugu, L.S. / 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*(P2U)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)28,2067
Polymers27,8903
Non-polymers3154
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-18 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.361, 56.860, 105.416
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: 20560.615 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*(P2U)P*GP*CP*AP*GP*C)-3')


Mass: 3634.355 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 , 3 types, 267 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG3350, potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2020
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→38.65 Å / Num. obs: 35493 / % possible obs: 99.8 % / Redundancy: 26.1 % / CC1/2: 0.999 / Rpim(I) all: 0.046 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.57-1.624.517520.3311.38199.7
8.6-38.6523.527010.007199.5

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Processing

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

4dk9


Resolution: 1.57→38.65 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 1766 5 %
Rwork0.1883 33526 -
obs0.1896 35292 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.22 Å2 / Biso mean: 28.3962 Å2 / Biso min: 11.32 Å2
Refinement stepCycle: final / Resolution: 1.57→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 486 19 270 2001
Biso mean--36.29 40.37 -
Num. residues----168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.610.36661340.3212495262998
1.61-1.660.29061320.290625632695100
1.66-1.710.31091370.28825502687100
1.71-1.770.30051560.27292510266699
1.77-1.850.27611480.238525442692100
1.85-1.930.35161210.31222538265998
1.93-2.030.25221420.209725662708100
2.03-2.160.27241480.21282531267999
2.16-2.330.18621210.19882571269299
2.33-2.560.23031260.176226012727100
2.56-2.930.21371390.16626322771100
2.93-3.690.15991250.14262635276099
3.69-38.650.161370.154927902927100
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)
13.1417-0.98290.38473.4840.23641.4612-0.0913-0.10050.24730.05120.07650.0551-0.12370.00760.00830.1216-0.0033-0.00180.1608-0.00730.1198.719420.940418.8345
23.28221.6915-0.77853.5264-0.60841.4728-0.0173-0.1920.00390.22980.0739-0.21050.02960.1576-0.04990.15260.029-0.02380.2018-0.0210.134421.806213.35823.8616
38.2043-2.08110.59282.4657-0.35721.75910.02060.3110.2815-0.1524-0.01030.0623-0.112-0.0313-0.01780.1826-0.0246-0.00790.16980.01560.12927.733423.31647.847
45.96925.8761-5.60747.5805-6.24475.5475-0.5477-0.415-0.1991-1.55070.0335-0.80471.47261.3230.97370.4813-0.00810.13170.35880.05280.4573-0.0067-7.808821.7244
51.1074-0.8059-1.22075.4319-1.90313.4275-0.07210.0017-0.113-0.13790.27680.54220.2817-0.4812-0.16550.1592-0.0583-0.03780.21170.01320.215.73626.437115.7585
63.16491.3599-1.94599.05692.73242.7935-0.20410.4284-0.2743-0.03660.4434-0.9210.44610.5787-0.11810.23530.04440.0140.31-0.08230.229620.36444.61157.1694
73.57950.52143.32432.3956-0.44363.57530.41510.2648-0.06230.21020.66010.64050.8088-0.974-0.96650.4637-0.02530.04250.43970.09040.323614.702-2.21245.2713
89.36221.4972-2.71386.1324-4.22953.1794-0.3626-0.2335-0.0942-0.09730.32750.34250.3729-0.07680.0970.15480.0058-0.00610.1494-0.00210.158112.4799-0.164621.9778
96.87285.24466.40984.07184.31079.1424-0.6354-0.94681.259-0.84360.09180.7377-0.0811-0.04130.5370.2113-0.0310.00180.3950.03730.5142-3.8938-0.198324.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 437:474)A437 - 474
2X-RAY DIFFRACTION2(chain A and resid 475:525)A475 - 525
3X-RAY DIFFRACTION3(chain A and resid 526:580)A526 - 580
4X-RAY DIFFRACTION4(chain C and resid 1:4)C1 - 4
5X-RAY DIFFRACTION5(chain C and resid 5:8)C5 - 8
6X-RAY DIFFRACTION6(chain C and resid 9:12)C9 - 12
7X-RAY DIFFRACTION7(chain D and resid 1:4)D1 - 4
8X-RAY DIFFRACTION8(chain D and resid 5:8)D5 - 8
9X-RAY DIFFRACTION9(chain D and resid 9:12)D9 - 12

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