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- PDB-7jl5: Crystal structure of human NEIL3 tandem zinc finger GRF domains -

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Basic information

Entry
Database: PDB / ID: 7jl5
TitleCrystal structure of human NEIL3 tandem zinc finger GRF domains
ComponentsEndonuclease 8-like 3
KeywordsDNA BINDING PROTEIN / DNA binding / zinc finger
Function / homology
Function and homology information


Defective Base Excision Repair Associated with NEIL3 / NEIL3-mediated resolution of ICLs / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / DNA-(apurinic or apyrimidinic site) endonuclease activity ...Defective Base Excision Repair Associated with NEIL3 / NEIL3-mediated resolution of ICLs / MCM complex binding / DNA N-glycosylase activity / bubble DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / interstrand cross-link repair / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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. ...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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRodriguez, A.A. / Wojtaszek, J.L. / Williams, R.S. / Eichman, B.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131071 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01ES102765 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: An autoinhibitory role for the GRF zinc finger domain of DNA glycosylase NEIL3.
Authors: Rodriguez, A.A. / Wojtaszek, J.L. / Greer, B.H. / Haldar, T. / Gates, K.S. / Williams, R.S. / Eichman, B.F.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 25, 2020Group: 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 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease 8-like 3
B: Endonuclease 8-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4866
Polymers24,2242
Non-polymers2624
Water00
1
A: Endonuclease 8-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2433
Polymers12,1121
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endonuclease 8-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2433
Polymers12,1121
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.494, 93.494, 63.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4

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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: 12111.967 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEIL3 / Plasmid: pMCSG9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8TAT5, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 57.15 % / Mosaicity: 0.46 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13020 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 40.85 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.02 / Rrim(I) all: 0.043 / Χ2: 0.759 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.656 / Num. unique obs: 435 / CC1/2: 0.84 / Rpim(I) all: 0.344 / Rrim(I) all: 0.742 / Χ2: 0.819 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→34.95 Å / SU ML: 0.3803 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.7932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 1276 9.8 %
Rwork0.2268 11742 -
obs0.2307 13018 78.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.86 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 4 0 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341366
X-RAY DIFFRACTIONf_angle_d0.67531846
X-RAY DIFFRACTIONf_chiral_restr0.0497186
X-RAY DIFFRACTIONf_plane_restr0.0054246
X-RAY DIFFRACTIONf_dihedral_angle_d15.473459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.3057590.2708469X-RAY DIFFRACTION27.69
2.7-2.820.2082730.3093715X-RAY DIFFRACTION42.78
2.82-2.970.33571170.31065X-RAY DIFFRACTION65.16
2.97-3.160.38321480.29481288X-RAY DIFFRACTION78.09
3.16-3.40.38041670.27231553X-RAY DIFFRACTION94.82
3.4-3.750.24891820.22921698X-RAY DIFFRACTION99.84
3.75-4.290.22371810.1831687X-RAY DIFFRACTION100
4.29-5.40.18631710.17931642X-RAY DIFFRACTION100
5.4-34.950.29291780.23671625X-RAY DIFFRACTION96.52
Refinement TLS params.Method: refined / Origin x: 8.72658801482 Å / Origin y: -22.9166255705 Å / Origin z: 18.0976214189 Å
111213212223313233
T0.160628461419 Å20.0281507281701 Å2-0.0126951677026 Å2-0.322521467726 Å20.0849431285355 Å2--0.302649954492 Å2
L1.55830373961 °2-0.214226373313 °2-1.25846396805 °2-0.312362884109 °20.467063007374 °2--1.87613392374 °2
S0.0428038899428 Å °-0.0248100116167 Å °-0.0803625488663 Å °-0.0541385727785 Å °0.0401882644748 Å °0.0403557231055 Å °0.00719474968979 Å °-0.287043319208 Å °-0.122656362322 Å °
Refinement TLS groupSelection details: all

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