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- PDB-7z5a: Crystal structure of the trapped complex of mouse Endonuclease VI... -

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Basic information

Entry
Database: PDB / ID: 7z5a
TitleCrystal structure of the trapped complex of mouse Endonuclease VIII-LIKE 3 (mNEIL3) and hairpin DNA with 5'overhang
Components
  • DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3')
  • Endonuclease 8-like 3
KeywordsDNA BINDING PROTEIN / Ap-ICL / DNA crosslink repair / NEIL3 / BER
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSilhan, J. / Huskova, A.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of SciencesRVO: 61388963 Czech Republic
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model.
Authors: Huskova, A. / Dinesh, D.C. / Srb, P. / Boura, E. / Veverka, V. / Silhan, J.
History
DepositionMar 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Endonuclease 8-like 3
E: DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3653
Polymers39,2992
Non-polymers651
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, NaBH3CN, gel filtration, Trapped covalent complex mNEIL3:DNA was subjected to size-exclusion column: Superdex 200 increase 10/300 GL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area15660 Å2
Unit cell
Length a, b, c (Å)56.117, 71.528, 94.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 33579.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neil3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8K203, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3')


Mass: 5719.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM PIPES pH = 7.5 4% (w/v) PEG 8000 20 mM MgCl2 1 mM Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.26→36.13 Å / Num. obs: 179306 / % possible obs: 99.96 % / Redundancy: 5.89 % / Biso Wilson estimate: 46.91 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1904 / Rrim(I) all: 0.2008 / Net I/σ(I): 9.11
Reflection shellResolution: 2.26→2.341 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 1800 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W0F

3w0f


Resolution: 2.28→36.13 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 883 4.98 %
Rwork0.2374 16859 -
obs0.238 17742 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.98 Å2 / Biso mean: 41.8284 Å2 / Biso min: 18.21 Å2
Refinement stepCycle: final / Resolution: 2.28→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 321 0 124 2484
Biso mean---40.84 -
Num. residues----280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.420.34751380.30532726286498
2.42-2.610.36241360.266628032939100
2.61-2.870.291400.243628082948100
2.87-3.290.27251440.244128322976100
3.29-4.140.23091430.24962728287196
4.14-36.130.20341820.201429623144100

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