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- PDB-8ftj: Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosy... -

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Basic information

Entry
Database: PDB / ID: 8ftj
TitleCrystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')
  • DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')
  • Endonuclease 8-like 1
KeywordsDNA BINDING PROTEIN/DNA / base-excision repair enzyme / DNA glycosylase / DNA binding protein / DNA binding protein-DNA complex
Function / homology
Function and homology information


negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / 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 / base-excision repair, gap-filling / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal 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 / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTomar, R. / Sharma, P. / Harp, J.M. / Egli, M. / Stone, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 ES-029357 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase.
Authors: Tomar, R. / Minko, I.G. / Sharma, P. / Kellum, A.H. / Lei, L. / Harp, J.M. / Iverson, T.M. / Lloyd, R.S. / Egli, M. / Stone, M.P.
History
DepositionJan 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 8-like 1
D: DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')
F: DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9959
Polymers41,5213
Non-polymers4746
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.662, 83.662, 130.442
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-306-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endonuclease 8-like 1 / DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease ...DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease VIII-like 1 / FPG1 / Nei homolog 1 / NEH1 / Nei-like protein 1


Mass: 33641.414 Da / Num. of mol.: 1 / Mutation: P2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEIL1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FI4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules DF

#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')


Mass: 3838.506 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: YB9 is modeled into the chain D of DNA template strand at position 297; basically urea moiety is covalently linked to ring-opened deoxyribose in YB9 residue ie. YB9 is modified nucleotide in ...Details: YB9 is modeled into the chain D of DNA template strand at position 297; basically urea moiety is covalently linked to ring-opened deoxyribose in YB9 residue ie. YB9 is modified nucleotide in DNA template strand (Chain D)
Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')


Mass: 4040.647 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Complementary DNA strand (Chain F) to template strand (chain D)
Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 133 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.01 M magnesium sulfate and 1.8 M lithium sulfate, 0.05 M sodium cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21210 / % possible obs: 99.3 % / Redundancy: 15.5 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.06 / Rsym value: 0.23 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 1025 / CC1/2: 0.74 / Rpim(I) all: 0.41 / Rsym value: 1.51 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000v721.2data reduction
HKL-2000v721.2data scaling
Coot0.9.8.4 EL (ccp4)model building
PHENIX1.20.1_4487refinement
PHASER1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.83 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1075 5.11 %
Rwork0.2008 19968 -
obs0.2029 21043 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 386 163 127 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782780
X-RAY DIFFRACTIONf_angle_d0.94013859
X-RAY DIFFRACTIONf_chiral_restr0.051397
X-RAY DIFFRACTIONf_plane_restr0.0102422
X-RAY DIFFRACTIONf_dihedral_angle_d22.14731093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.26921350.21422409X-RAY DIFFRACTION97.55
2.4-2.530.32311330.2292433X-RAY DIFFRACTION98.2
2.53-2.690.32111310.24172434X-RAY DIFFRACTION98.16
2.69-2.90.34891360.24452448X-RAY DIFFRACTION98.44
2.9-3.190.24431310.22262479X-RAY DIFFRACTION99.2
3.19-3.650.24751310.19322514X-RAY DIFFRACTION99.21
3.65-4.590.18871210.15682566X-RAY DIFFRACTION99.74
4.6-39.830.20051570.19642685X-RAY DIFFRACTION98.99

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