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- PDB-8b9n: Crystal structure of NEI domain of mouse NEIL3 trapped in covalen... -

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Basic information

Entry
Database: PDB / ID: 8b9n
TitleCrystal structure of NEI domain of mouse NEIL3 trapped in covalent complex with ssDNA with abasic site
Components
  • Endonuclease 8-like 3
  • ssDNA with abasic site
KeywordsDNA BINDING PROTEIN / NEIL3 / NEI / ssDNA / abasic site
Function / homology
Function and homology information


Cleavage of the damaged purine / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair ...Cleavage of the damaged purine / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / single-stranded DNA binding / chromosome / double-stranded DNA binding / damaged DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / Zinc finger, DNA glycosylase/AP lyase-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain ...Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / Zinc finger, DNA glycosylase/AP lyase-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8-like 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlima, M. / Boura, E. / Silhan, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of NEI domain of mouse NEIL3 trapped in covalent complex with ssDNA with abasic site
Authors: Klima, M. / Boura, E. / Silhan, J.
History
DepositionOct 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 8-like 3
B: ssDNA with abasic site
C: Endonuclease 8-like 3
D: ssDNA with abasic site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3206
Polymers71,1894
Non-polymers1312
Water3,855214
1
A: Endonuclease 8-like 3
B: ssDNA with abasic site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,5942
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endonuclease 8-like 3
D: ssDNA with abasic site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,5942
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.056, 75.056, 220.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

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Components

#1: Protein Endonuclease 8-like 3 / DNA glycosylase FPG2 / DNA glycosylase/AP lyase Neil3 / Endonuclease VIII-like 3 / Nei-like protein 3


Mass: 32089.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neil3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8K203, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain ssDNA with abasic site


Mass: 3505.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES.Na pH 7.0, 5 mM MgCl2, 25% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→38.22 Å / Num. obs: 43404 / % possible obs: 95.59 % / Redundancy: 23.2 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2192 / Rpim(I) all: 0.04674 / Rrim(I) all: 0.2244 / Net I/σ(I): 12.15
Reflection shellResolution: 2→2.072 Å / Redundancy: 15 % / Rmerge(I) obs: 2.119 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4124 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.5463 / Rrim(I) all: 2.192 / % possible all: 96.28

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W0F

3w0f


Resolution: 2→38.22 Å / SU ML: 0.2753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 2082 4.99 %random selection
Rwork0.2391 39632 --
obs0.2411 41714 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.23 Å2
Refinement stepCycle: LAST / Resolution: 2→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 105 88 214 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543975
X-RAY DIFFRACTIONf_angle_d0.68375373
X-RAY DIFFRACTIONf_chiral_restr0.048600
X-RAY DIFFRACTIONf_plane_restr0.0056668
X-RAY DIFFRACTIONf_dihedral_angle_d13.8571506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33951350.33022572X-RAY DIFFRACTION94.92
2.05-2.10.30521420.28142691X-RAY DIFFRACTION99.02
2.1-2.150.31881420.26512699X-RAY DIFFRACTION99.86
2.15-2.220.31251430.26522712X-RAY DIFFRACTION99.86
2.22-2.290.4765630.34981241X-RAY DIFFRACTION45.87
2.29-2.370.33611430.25112714X-RAY DIFFRACTION99.97
2.37-2.470.29851440.2362724X-RAY DIFFRACTION99.9
2.47-2.580.26541440.22142740X-RAY DIFFRACTION100
2.58-2.710.30891430.23162732X-RAY DIFFRACTION99.97
2.71-2.880.27861450.23662755X-RAY DIFFRACTION99.93
2.88-3.110.27011460.24782770X-RAY DIFFRACTION99.97
3.11-3.420.29191450.23742780X-RAY DIFFRACTION99.93
3.42-3.910.26061390.24182639X-RAY DIFFRACTION94.72
3.91-4.930.22091490.2032831X-RAY DIFFRACTION99.23
4.93-38.220.28281590.24083032X-RAY DIFFRACTION99.94

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