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- PDB-6lwo: Crystal structure of human NEIL1(R242, Y244H) bound to duplex DNA... -

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Basic information

Entry
Database: PDB / ID: 6lwo
TitleCrystal structure of human NEIL1(R242, Y244H) 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


negative regulation of nuclease 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...negative regulation of nuclease 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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)123,78010
Polymers123,6889
Non-polymers921
Water4,990277
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')


Theoretical massNumber of molelcules
Total (without water)41,2293
Polymers41,2293
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-14 kcal/mol
Surface area15840 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3214
Polymers41,2293
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-15 kcal/mol
Surface area16110 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)41,2293
Polymers41,2293
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-15 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.926, 109.447, 170.603
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: 33304.203 Da / Num. of mol.: 3 / Mutation: Y244H
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.: 277 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
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: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 47463 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Χ2: 1.561 / Net I/σ(I): 14.1 / Num. measured all: 281914
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.48-2.526.10.99723580.7070.4461.0941.433100
2.52-2.576.10.8323290.7970.3710.9111.429100
2.57-2.626.10.72823470.8280.3250.7991.453100
2.62-2.676.10.56823190.8930.2530.6231.46100
2.67-2.736.10.47523620.9130.2120.5211.462100
2.73-2.796.10.3723530.9390.1650.4061.454100
2.79-2.866.10.28823370.9630.1280.3161.541100
2.86-2.946.10.23323970.9750.1030.2551.558100
2.94-3.036.10.18623420.9850.0820.2041.628100
3.03-3.126.10.14223600.990.0630.1551.685100
3.12-3.246.10.10823430.9930.0480.1191.643100
3.24-3.376.10.08923540.9950.0390.0981.647100
3.37-3.5260.07323790.9960.0320.081.652100
3.52-3.760.06223770.9970.0270.0681.666100
3.7-3.9460.05923870.9970.0260.0641.743100
3.94-4.245.80.05623870.9970.0250.0611.599100
4.24-4.675.60.05323920.9970.0250.0591.60999.6
4.67-5.345.50.05324200.9960.0240.0581.52199.6
5.34-6.735.50.04624510.9980.0210.0511.60199.8
6.73-505.30.0424690.9980.0190.0451.42595.4

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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: 2.51→36.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.579 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2466 5.2 %RANDOM
Rwork0.2027 ---
obs0.2048 44932 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.11 Å2 / Biso mean: 75.438 Å2 / Biso min: 31.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---2.15 Å20 Å2
3---3.04 Å2
Refinement stepCycle: final / Resolution: 2.51→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 1575 6 277 7588
Biso mean--76.19 65.71 -
Num. residues----826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127639
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186341
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.54110625
X-RAY DIFFRACTIONr_angle_other_deg1.3221.78114590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6635734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10419.971343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69615910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.91564
X-RAY DIFFRACTIONr_chiral_restr0.0790.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021888
LS refinement shellResolution: 2.51→2.573 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 137 -
Rwork0.291 2684 -
obs--80.19 %
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)
12.84882.26020.28866.40451.71121.6731-0.19380.1897-0.0027-0.22420.2655-0.40780.01150.0888-0.07170.02410.00820.03460.08450.04710.1732-8.69-8.89435.793
210.1132-3.4452-3.20343.97711.16273.90650.21610.9196-0.2278-0.6344-0.1412-0.17370.02350.2742-0.07490.3775-0.04760.08430.4107-0.0710.4853-1.24-15.93319.791
37.3635-2.6668-0.073210.17983.26983.8152-0.0064-0.087-0.3343-0.42190.2922-0.15110.3772-0.2127-0.28580.321-0.06150.23920.4860.06580.44943.852-18.32320.258
45.1088-2.0078-0.03824.2165-0.23753.2409-0.2341-0.231-0.39650.22310.14580.12920.1405-0.00670.08840.06270.04910.02640.0926-0.02470.08-29.3148.11751.522
58.32470.277-2.26393.23020.34224.586-0.1775-0.75580.18850.57390.14680.3362-0.181-0.14610.03070.36860.09650.03270.4843-0.00320.2444-35.92517.42166.136
68.67631.9422.09595.0088-1.38311.5053-0.3384-0.9272-0.49770.86970.2947-0.25790.0121-0.2890.04370.36190.19320.19850.41080.05510.3663-40.71415.53368.342
75.6739-0.5225-2.75622.4511-0.43384.75040.26820.0174-0.1073-0.4525-0.24470.1165-0.0861-0.2722-0.02360.86560.1344-0.08220.7635-0.17630.1827-43.8618.6364.398
87.6093-0.20783.92662.0386-0.28535.5726-0.01930.0715-1.0308-0.31290.0960.0169-0.0971-0.0392-0.07670.75920.04150.01680.90970.00660.5696-37.14-6.362-0.785
97.7224-1.20861.27424.9046-2.52711.8897-0.0332-0.353-0.36380.2360.01330.17440.1649-0.12920.01990.73940.08580.05390.9127-0.05260.4871-32.572-7.741.546
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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