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

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Basic information

Entry
Database: PDB / ID: 6lwj
TitleCrystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing dihydrouracil (DHU)
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(UDH)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 / 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 / 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 / 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 / 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: 2.83 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*(UDH)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*(UDH)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*(UDH)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)123,59410
Polymers123,5029
Non-polymers921
Water2,810156
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(UDH)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)41,2594
Polymers41,1673
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-14 kcal/mol
Surface area15890 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(UDH)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)41,1673
Polymers41,1673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-14 kcal/mol
Surface area15880 Å2
MethodPISA
3
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(UDH)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)41,1673
Polymers41,1673
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-13 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.968, 108.939, 168.315
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: 33260.168 Da / Num. of mol.: 3 / 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*(UDH)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3890.538 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.99 %
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: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 33126 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Χ2: 0.977 / Net I/σ(I): 5.5 / Num. measured all: 210859
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.82-2.876.20.7216160.8140.3130.7870.528100
2.87-2.926.60.61616290.8510.2570.6680.54599.9
2.92-2.986.50.53616180.8920.2250.5820.56399.9
2.98-3.046.60.47416350.9150.1980.5140.596100
3.04-3.16.50.38416410.9280.1620.4170.63199.9
3.1-3.186.40.29116140.9590.1240.3160.71799.9
3.18-3.266.30.24516230.9660.1060.2670.78499.9
3.26-3.346.20.2216620.9690.0960.240.83799.8
3.34-3.445.90.20316240.9320.0920.2231.07599.9
3.44-3.556.20.1616490.9810.0690.1740.984100
3.55-3.686.70.15716380.9870.0660.171.28499.9
3.68-3.836.70.12516410.9880.0520.1361.143100
3.83-46.60.1216570.990.0510.131.34899.9
4-4.216.60.116390.9930.0420.1081.352100
4.21-4.486.10.09216600.990.040.1011.439100
4.48-4.826.30.08316810.9930.0360.091.311100
4.82-5.316.70.07816710.9940.0320.0851.201100
5.31-6.076.50.07216990.9950.030.0780.968100
6.07-7.6560.06317170.9960.0280.0690.935100
7.65-505.90.05518120.9970.0250.0611.24799.7

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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: 2.83→49.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 28.916 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.438 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1628 4.9 %RANDOM
Rwork0.1998 ---
obs0.2018 31440 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.2 Å2 / Biso mean: 80.815 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å2-0 Å2
2---0.75 Å20 Å2
3---2.51 Å2
Refinement stepCycle: final / Resolution: 2.83→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 1572 6 156 7552
Biso mean--92.21 60.54 -
Num. residues----837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127733
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186417
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.54310746
X-RAY DIFFRACTIONr_angle_other_deg1.3831.78214770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1165746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46719.777358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18915924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6651569
X-RAY DIFFRACTIONr_chiral_restr0.0810.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027855
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021938
LS refinement shellResolution: 2.83→2.902 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.364 121 -
Rwork0.286 2137 -
obs--93.62 %
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)
15.07072.32410.28934.18590.61134.1853-0.14510.233-0.3661-0.29210.1961-0.07980.23660.109-0.05110.1264-0.04010.04110.05110.00950.113629.7058.27133.413
27.3596-1.2171-2.37574.4901-0.62023.8714-0.16430.81960.2835-0.64030.1736-0.066-0.52380.1089-0.00920.4212-0.0818-0.01850.4773-0.00270.286236.11317.67718.864
38.2009-1.26870.64693.04350.21459.92490.08161.0052-0.3917-0.84670.11880.27220.1159-0.0273-0.20040.4053-0.17860.13770.3659-0.08830.355540.79715.66916.578
43.0893-2.19060.05616.4348-1.61981.8-0.1794-0.10680.05320.28360.27040.52830.0278-0.0806-0.0910.0366-0.00230.06990.0234-0.02250.2248.609-8.42949.04
54.3572-0.2038-2.8261.9381-0.55542.74070.351-1.44260.0730.9336-0.0290.4036-0.25060.4172-0.3220.6532-0.43040.17910.94210.02670.61971.161-15.24764.91
65.7590.64130.98169.7802-2.84735.05160.04010.11960.12810.3950.16290.05840.43690.4719-0.20290.4075-0.0020.35490.3759-0.02780.5017-3.838-17.86964.358
76.12591.2975-3.6282.367-0.71116.04240.11020.04880.30310.1117-0.11670.0142-0.03620.49530.00640.8986-0.1431-0.03710.56350.1710.361942.5429.86480.61
87.4189-2.173-2.07690.86280.9773.63290.04660.1053-1.04830.2760.04060.03160.05720.1035-0.08730.8988-0.0509-0.19520.75970.10780.628637.118-5.72685.198
98.69811.2005-0.00875.45372.84992.6679-0.05430.4194-0.2589-0.2552-0.1066-0.06510.33930.16250.16090.691-0.08810.05620.66110.10510.406732.633-7.03682.731
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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