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- PDB-6lwp: Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA... -

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Basic information

Entry
Database: PDB / ID: 6lwp
TitleCrystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
  • Endonuclease 8-like 1
KeywordsDNA BINDING PROTEIN/DNA / Base lesion / Oxidative DNA damage / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / 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 / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity ...: / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / 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 / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsLiu, M.H. / Zhang, J. / Zhu, C.X. / Zhang, X.X. / Gao, Y.Q. / Yi, C.Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953201 China
National Natural Science Foundation of China (NSFC)21825701 China
CitationJournal: Nat Commun / Year: 2021
Title: DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes.
Authors: Liu, M. / Zhang, J. / Zhu, C. / Zhang, X. / Xiao, W. / Yan, Y. / Liu, L. / Zeng, H. / Gao, Y.Q. / Yi, C.
History
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
C: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
I: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,83710
Polymers123,7459
Non-polymers921
Water3,891216
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
C: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3404
Polymers41,2483
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area16020 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,2483
Polymers41,2483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-15 kcal/mol
Surface area16130 Å2
MethodPISA
3
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
I: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,2483
Polymers41,2483
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-14 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.938, 109.635, 171.944
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 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: 33323.250 Da / Num. of mol.: 3 / Mutation: Y244R
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
#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3908.528 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Oligo DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Mass: 4016.623 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Complementary strand / Source: (synth.) Escherichia coli (E. coli)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 41670 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.044 / Rrim(I) all: 0.101 / Χ2: 1.515 / Net I/σ(I): 11 / Num. measured all: 210229
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.64-2.695.20.99220320.7150.4681.0991.391100
2.69-2.735.30.81520820.7290.3850.9041.383100
2.73-2.795.30.70220310.7990.3310.7781.395100
2.79-2.845.20.55220660.8560.2610.6121.394100
2.84-2.915.20.44520490.8980.2110.4941.432100
2.91-2.975.20.36920880.9270.1750.411.452100
2.97-3.055.30.30420500.9510.1440.3381.473100
3.05-3.135.20.23920640.9680.1130.2651.549100
3.13-3.225.20.18120880.9820.0860.2011.596100
3.22-3.335.20.14720470.9860.070.1631.626100
3.33-3.445.20.11920690.990.0570.1321.667100
3.44-3.585.20.10220920.9920.0490.1141.611100
3.58-3.755.10.08520820.9940.0410.0951.616100
3.75-3.945.10.08120850.9940.0390.091.527100
3.94-4.194.90.07520970.9940.0370.0841.609100
4.19-4.514.70.06620900.9940.0340.0741.57799.9
4.51-4.974.50.06421210.9940.0330.0721.62499.9
4.97-5.694.60.06321200.9940.0320.0711.50699.6
5.69-7.164.80.05121440.9970.0260.0581.48799.6
7.16-504.50.04121730.9980.0210.0461.40695

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITY

5ity


Resolution: 2.64→36.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.665 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 2130 5.1 %RANDOM
Rwork0.2034 ---
obs0.2049 39478 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.13 Å2 / Biso mean: 81.84 Å2 / Biso min: 34.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å2-0 Å2
2--0.34 Å2-0 Å2
3---1.21 Å2
Refinement stepCycle: final / Resolution: 2.64→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 1575 6 216 7673
Biso mean--97.69 65.73 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127795
X-RAY DIFFRACTIONr_bond_other_d0.0030.0186498
X-RAY DIFFRACTIONr_angle_refined_deg1.611.54510849
X-RAY DIFFRACTIONr_angle_other_deg1.3331.77614963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9035747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92819.889361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79115933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9521569
X-RAY DIFFRACTIONr_chiral_restr0.0810.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021936
LS refinement shellResolution: 2.64→2.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 134 -
Rwork0.289 2805 -
all-2939 -
obs--97.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.93192.34050.39716.37091.83541.6059-0.19570.18070.0158-0.22720.2865-0.3670.04110.1344-0.09080.0226-0.00760.01760.02410.02680.2985-8.65-8.95336.155
29.3357-3.0216-3.28513.93410.64944.7950.31181.1626-0.2652-0.7669-0.2340.179-0.21750.3035-0.07780.4419-0.04550.07890.4091-0.08840.6277-1.24-15.97320.085
35.8366-1.6533-0.33959.54033.37515.3038-0.0441-0.1473-0.1122-0.58680.3504-0.0740.3665-0.3708-0.30620.4105-0.06630.230.47770.01350.57063.961-18.46620.547
46.1063-2.397-0.22444.6410.19233.4208-0.259-0.2991-0.40470.3060.16670.19740.16910.03820.09230.07410.04030.0220.0387-0.02840.2526-29.2798.15551.888
58.58790.949-3.27453.84120.89234.2596-0.1856-0.68470.25480.52770.08940.3325-0.17350.06280.09620.40950.1147-0.05120.51580.02790.3859-35.84817.56566.548
64.40590.84591.53382.9247-0.856413.687-0.4288-0.8123-0.33860.75140.3371-0.3682-0.1465-0.34810.09170.40740.23850.17110.41260.03370.5549-40.78315.78968.868
75.23550.3626-2.17022.2007-0.26644.71680.3081-0.0102-0.1309-0.3025-0.20570.00730.09470.1009-0.10230.93090.2396-0.12110.7285-0.18380.4462-43.4039.1773.734
88.8608-0.99834.68361.84970.78284.2267-0.1575-0.0692-0.6906-0.1890.1791-0.0075-0.0813-0.043-0.02160.849-0.01230.04050.93820.110.7181-37.139-6.54-0.827
95.98450.1313-0.02617.7947-3.53053.664-0.3706-0.1681-0.50490.42090.15970.32020.17920.1530.2110.83150.16560.06161.0262-0.1060.657-32.452-7.8381.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 290
2X-RAY DIFFRACTION2B1 - 13
3X-RAY DIFFRACTION3C1 - 13
4X-RAY DIFFRACTION4D2 - 290
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F1 - 13
7X-RAY DIFFRACTION7G2 - 289
8X-RAY DIFFRACTION8H1 - 13
9X-RAY DIFFRACTION9I1 - 13

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