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- PDB-7omk: The NMR structure of the Zf-GRF domains from the mouse Endonuclea... -

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Basic information

Entry
Database: PDB / ID: 7omk
TitleThe NMR structure of the Zf-GRF domains from the mouse Endonuclease VIII-LIKE 3 (mNEIL3)
ComponentsEndonuclease 8-like 3
KeywordsDNA BINDING PROTEIN / Zinc Finger / NEIL3-GRF / DNA repair / DNA damage
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
Endonuclease 8-like 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsDinesh, D.C. / Huskova, A. / Srb, P. / Veverka, V. / Silhan, J.
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
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease 8-like 3


Theoretical massNumber of molelcules
Total (without water)10,8191
Polymers10,8191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7110 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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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: 10818.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neil3 / Plasmid: pSUMO / Details (production host): N-terminal His-SUMO tag / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): STAR
References: UniProt: Q8K203, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D HN(CO)CA
191isotropic13D CBCA(CO)NH
181isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
1111isotropic13D (H)CCH-TOCSY
1101isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution / Contents: 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O
Details: 250uM [U-13C; U-15N] mNEIL3-GRF, 12.5 mM sodium phosphate, 50 mM sodium chloride, 1mM TCEP
Label: 13C_15N / Solvent system: 95% H2O/5% D2O
SampleConc.: 250 uM / Component: NEIL3-GRF / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 250 uM [U-13C; U-15N] mNEIL3-GRF, 12.5 mM sodium phosphate, 50 mM sodium chloride, 1mM TCEP
Ionic strength: 50 mM / Label: NMR_sample / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospindata analysis
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAYASARAstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 35

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