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- PDB-6lwc: Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex ... -

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Basic information

Entry
Database: PDB / ID: 6lwc
TitleCrystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DSP)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: 2.91 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*(DSP)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*(DSP)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)82,4736
Polymers82,4736
Non-polymers00
Water99155
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DSP)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')


Theoretical massNumber of molelcules
Total (without water)41,2363
Polymers41,2363
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area16140 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DSP)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)41,2363
Polymers41,2363
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-10 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.757, 143.614, 71.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 33260.168 Da / Num. of mol.: 2 / Mutation: P2G, E3Q
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*(DSP)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3959.560 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oligo DNA containing Sp / 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.: 2 / Source method: obtained synthetically / Details: Complementary strand / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
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: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. obs: 20492 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Rrim(I) all: 0.089 / Χ2: 1.571 / Net I/σ(I): 14.2 / Num. measured all: 119078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.91-2.9660.9610230.8850.4271.0521.431100
2.96-3.016.10.7959950.8730.3510.871.422100
3.01-3.076.10.77210250.8620.3420.8461.431100
3.07-3.136.10.58410010.9280.2570.641.501100
3.13-3.26.10.44110150.9570.1950.4831.535100
3.2-3.286.10.36210220.9560.160.3971.617100
3.28-3.366.10.27110130.9770.1190.2971.661100
3.36-3.456.10.2110160.9860.0920.231.662100
3.45-3.5560.16210300.990.0720.1781.66499.9
3.55-3.676.10.1310140.9960.0570.1431.705100
3.67-3.860.10710080.9950.0480.1171.781100
3.8-3.9560.09210140.9960.0410.1011.80699.9
3.95-4.135.90.08210350.9960.0370.091.71299.9
4.13-4.355.80.06610200.9970.030.0731.611100
4.35-4.625.70.06110360.9970.0280.0671.44699.8
4.62-4.975.40.0610480.9960.0280.0671.428100
4.97-5.475.30.05910400.9950.0280.0651.43299.9
5.47-6.275.20.05710520.9960.0280.0641.43999.7
6.27-7.895.40.05110610.9970.0240.0571.46599.4
7.89-504.90.04410240.9970.0210.0491.6288.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITY

5ity


Resolution: 2.91→37.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 34.042 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 983 4.8 %RANDOM
Rwork0.1906 ---
obs0.193 19472 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 256.04 Å2 / Biso mean: 115.328 Å2 / Biso min: 53.48 Å2
Baniso -1Baniso -2Baniso -3
1--7.09 Å2-0 Å20 Å2
2--4.39 Å2-0 Å2
3---2.7 Å2
Refinement stepCycle: final / Resolution: 2.91→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 1058 0 55 5234
Biso mean---89.92 -
Num. residues----579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125414
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184579
X-RAY DIFFRACTIONr_angle_refined_deg1.781.5527535
X-RAY DIFFRACTIONr_angle_other_deg1.3371.76410535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1525521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98219.647255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09315673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0851550
X-RAY DIFFRACTIONr_chiral_restr0.0770.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025491
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021365
LS refinement shellResolution: 2.91→2.981 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.301 70 -
Rwork0.276 1297 -
obs--91.26 %
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)
16.8710.09431.93062.13710.10263.73970.0902-0.6119-0.39020.161-0.01780.24990.391-0.1847-0.07250.0777-0.02290.0350.06140.0240.0662-68.013311.252100.869
23.9182-0.1361-2.03712.2876-2.20979.4448-0.2798-0.1836-0.92570.2330.09140.08471.2963-0.28830.18840.578-0.14330.04520.42850.07810.6307-75.311295.409106.566
310.94821.410.88723.20091.27449.79550.0992-0.1607-0.9074-0.3833-0.1480.48950.0596-0.54110.04880.6615-0.03760.16060.41330.31690.6102-77.85295.53111.219
44.9750.5086-1.45746.60191.31325.33740.3979-0.05720.8447-0.2215-0.2615-0.1526-0.82580.0966-0.13640.4209-0.09150.16410.20370.0020.239-64.215334.4279.71
52.2753-1.7793.00662.7371-0.26618.4005-0.12520.32190.53630.2601-0.144-0.371-0.8221.07980.26911.3258-0.05720.06810.95130.16790.8749-53.96348.64271.826
63.77030.2045-2.719612.72887.94267.66850.7915-0.2680.9229-0.59640.1287-0.6175-0.7499-0.1773-0.92021.2559-0.11560.11530.8920.34590.8979-55.794350.73466.939
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 - 289
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F1 - 13

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