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- PDB-7kzg: Human MBD4 glycosylase domain bound to DNA containing oxacarbeniu... -

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Basic information

Entry
Database: PDB / ID: 7kzg
TitleHuman MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose
Components
  • DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 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 10, 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*(NR1)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)28,37511
Polymers27,7803
Non-polymers5958
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-44 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.465, 56.414, 102.733
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*(NR1)P*GP*CP*AP*GP*C)-3')


Mass: 3524.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.) Homo sapiens (human)

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Non-polymers , 6 types, 243 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG1000, HEPES

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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: Oct 24, 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: 1.68→37.98 Å / Num. obs: 28121 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.994 / Rpim(I) all: 0.091 / Rrim(I) all: 0.333 / Net I/σ(I): 10.2 / Num. measured all: 367050 / Scaling rejects: 251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.7113.31907714290.4161.7236.4031.5100
9.05-37.9811.526432300.9730.030.09735.399.1

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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: 1.68→37.98 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 1429 5.1 %
Rwork0.1681 26617 -
obs0.1699 28046 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.18 Å2 / Biso mean: 27.4813 Å2 / Biso min: 9.49 Å2
Refinement stepCycle: final / Resolution: 1.68→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 478 37 242 1968
Biso mean--37.81 38.93 -
Num. residues----168
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 (%)
1.68-1.740.26621430.26132600274399
1.74-1.810.27281460.235426322778100
1.81-1.890.22291320.21612596272898
1.89-1.990.2261460.191726212767100
1.99-2.120.21791250.173926592784100
2.12-2.280.20071540.17226502804100
2.28-2.510.19061510.16162635278699
2.51-2.870.20581400.158726902830100
2.87-3.620.1971460.15262682282899
3.62-37.980.18711460.15082852299899
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)
12.8541-0.32621.19181.79011.04282.49860.0405-0.30530.49720.0811-0.05880.0725-0.2435-0.1931-0.0090.1740.00920.00140.1887-0.00480.20675.215217.849317.252
22.62521.21010.08785.30480.22652.8507-0.0495-0.1089-0.0707-0.07130.05660.0913-0.0359-0.0554-0.00970.08910.0134-0.00760.12240.00730.085813.59996.322917.8962
31.96252.74721.77744.63810.94495.90290.2776-0.39490.24550.5196-0.19770.29830.0392-0.1175-0.04870.19740.03630.04230.138-0.00310.124812.63856.31527.6359
44.13940.0939-0.12974.23760.3024.00780.048-0.2630.09390.4924-0.0139-0.3454-0.12820.1189-0.04610.1675-0.0081-0.04270.1465-0.03440.138427.05759.617524.2087
52.92583.42210.09774.67071.42446.74580.0116-0.5645-0.18980.34610.0183-0.2502-0.0470.24410.00040.22190.0524-0.02720.17540.02270.139320.5953-2.790425.9434
62.99182.7884-1.42056.6237-2.64643.5648-0.0491-0.0022-0.0596-0.1549-0.0025-0.30470.11080.23860.06490.09460.0173-0.00910.1252-0.00660.112524.12584.081817.0816
76.19210.67811.18354.0923-0.7455.36990.06330.39870.1783-0.0389-0.0502-0.2372-0.09890.29180.01110.1260.01380.00960.13390.0170.096521.916211.24817.3057
84.3894-0.98871.24244.72561.72082.37080.12790.1070.0982-0.1734-0.07160.26040.0861-0.2487-0.05640.1183-0.0038-0.01080.13160.02830.110210.80912.05868.4688
94.41920.90966.21831.72641.70258.9246-0.27110.12450.3632-0.26870.0109-0.2531-0.61490.14640.26420.2115-0.00030.01420.16090.05340.19528.233419.83785.0226
106.64212.7686-2.53014.3344-5.22536.43120.03570.2777-0.2377-0.4710.0062-0.14750.88830.1085-0.0810.24970.0542-0.05860.145-0.01120.11145.18948.26733.5574
114.317-2.52262.0214.394-2.37536.53120.1364-0.0789-0.1001-0.22370.09190.37610.193-0.4175-0.23990.1458-0.0165-0.01780.17380.01410.1767-1.539513.17628.2296
120.9869-0.63340.46980.90251.63227.77130.17760.1420.7818-1.2478-0.2863-0.4741-1.0180.7334-0.07450.42080.04190.06280.47640.14050.4796-2.832425.42586.9829
130.86710.9272-0.10553.0846-1.37073.0575-0.29060.2325-0.4928-0.44370.20560.05010.588-0.27620.15190.2158-0.03440.01770.163-0.00990.28259.1692-8.270313.8219
144.87150.35960.42721.64130.37881.3961-0.17810.0831-0.0641-0.41980.33620.54160.4838-0.2357-0.02080.2816-0.0621-0.03730.18440.10370.32537.973-9.989816.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 437 through 455 )A437 - 455
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 470 )A456 - 470
3X-RAY DIFFRACTION3chain 'A' and (resid 471 through 484 )A471 - 484
4X-RAY DIFFRACTION4chain 'A' and (resid 485 through 495 )A485 - 495
5X-RAY DIFFRACTION5chain 'A' and (resid 496 through 508 )A496 - 508
6X-RAY DIFFRACTION6chain 'A' and (resid 509 through 525 )A509 - 525
7X-RAY DIFFRACTION7chain 'A' and (resid 526 through 538 )A526 - 538
8X-RAY DIFFRACTION8chain 'A' and (resid 539 through 548 )A539 - 548
9X-RAY DIFFRACTION9chain 'A' and (resid 549 through 555 )A549 - 555
10X-RAY DIFFRACTION10chain 'A' and (resid 556 through 560 )A556 - 560
11X-RAY DIFFRACTION11chain 'A' and (resid 561 through 573 )A561 - 573
12X-RAY DIFFRACTION12chain 'A' and (resid 574 through 580 )A574 - 580
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 12 )C1 - 12
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 12 )D1 - 12

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