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- PDB-6lwb: Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex ... -

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Basic information

Entry
Database: PDB / ID: 6lwb
TitleCrystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing 5-hydroxyuracil (5-OHU)
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)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: 2.55 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*(OHU)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*(OHU)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*(OHU)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)123,6289
Polymers123,6289
Non-polymers00
Water4,684260
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)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)41,2093
Polymers41,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-13 kcal/mol
Surface area16040 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)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)41,2093
Polymers41,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-12 kcal/mol
Surface area16210 Å2
MethodPISA
3
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)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)41,2093
Polymers41,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-12 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.807, 109.236, 169.402
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: 33288.184 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*(OHU)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3904.521 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Oligo DNA containing OHU / 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 / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
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 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 45145 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.034 / Rrim(I) all: 0.093 / Χ2: 1.415 / Net I/σ(I): 12.3 / Num. measured all: 324137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.597.10.99122080.7880.3981.0691.248100
2.59-2.647.10.91222510.830.3650.9841.294100
2.64-2.697.20.75221970.8780.30.8111.29699.8
2.69-2.757.20.62822510.8980.2510.6771.313100
2.75-2.817.20.50222220.9290.20.5411.314100
2.81-2.877.20.39422470.9550.1570.4251.354100
2.87-2.947.20.30422120.9710.1210.3271.36899.7
2.94-3.027.20.2622310.9770.1030.281.373100
3.02-3.117.20.19122420.9870.0760.2061.408100
3.11-3.217.30.13622530.9940.0540.1461.43799.9
3.21-3.337.30.11422320.9950.0450.1231.52100
3.33-3.467.30.09222530.9960.0370.0991.542100
3.46-3.627.30.08422460.9960.0330.091.55100
3.62-3.817.30.08122520.9970.0320.0881.476100
3.81-4.057.30.08922730.9950.0350.0961.428100
4.05-4.367.30.0922850.9940.0360.0971.446100
4.36-4.87.20.08822630.9930.0350.0951.5100
4.8-5.497.10.06623240.9970.0260.0711.491100
5.49-6.9270.04523260.9980.0180.0491.41999.9
6.92-506.70.03523770.9990.0150.0381.49996.4

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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: 2.55→32.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.102 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2274 5 %RANDOM
Rwork0.2096 ---
obs0.2117 42812 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.57 Å2 / Biso mean: 77.872 Å2 / Biso min: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å2-0 Å2-0 Å2
2---2.06 Å20 Å2
3---3.89 Å2
Refinement stepCycle: final / Resolution: 2.55→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5735 1575 0 260 7570
Biso mean---66.49 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127649
X-RAY DIFFRACTIONr_bond_other_d0.0030.0186326
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.54210643
X-RAY DIFFRACTIONr_angle_other_deg1.3371.78114554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4435741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7319.797344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63215897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5551566
X-RAY DIFFRACTIONr_chiral_restr0.0790.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021901
LS refinement shellResolution: 2.553→2.619 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 161 -
Rwork0.309 3031 -
all-3192 -
obs--96.87 %
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)
12.84012.1982-0.12516.5008-1.84991.705-0.21740.1848-0.076-0.31470.28240.454-0.035-0.0789-0.06490.0382-0.002-0.04520.0427-0.03610.14368.614117.721204.754
29.499-2.01083.32462.7382-0.45233.53910.31070.7085-0.0648-0.7263-0.05850.2213-0.0122-0.3232-0.25220.4397-0.0328-0.10270.37020.05470.42221.194124.551188.627
36.3928-2.2531-0.51599.9901-2.79714.50950.0382-0.15830.2655-0.38240.15450.0032-0.39820.4838-0.19270.3691-0.0546-0.28680.4569-0.02080.3668-3.863127.17189.277
45.4409-2.6407-0.19064.63940.53493.7282-0.2626-0.28710.40860.36330.2648-0.1739-0.15110.1474-0.00220.09150.0593-0.03370.09420.00940.08629.42100.754220.52
58.55681.89382.74214.1267-0.82883.1613-0.1097-0.7266-0.16680.59220.179-0.17050.24720.184-0.06930.44280.088-0.02760.5419-0.04920.259636.0291.383235.197
69.70081.5415-1.43024.58830.23811.1284-0.0395-0.67410.37590.95360.3220.2570.13750.159-0.28250.40770.2019-0.18030.3682-0.08170.289140.793.435237.478
76.1352-0.51963.55181.8512-0.40266.16480.0109-0.0485-0.1004-0.058-0.0769-0.0147-0.0010.4550.0660.77690.13020.01250.6130.16660.289542.5199.475173.311
89.116-0.5051-2.90911.83770.20074.6090.04670.18460.5934-0.2178-0.01320.0293-0.11590.1018-0.03350.73210.0136-0.02530.76160.010.508436.957115.252168.368
98.6173-1.1874-0.37448.16292.83482.2837-0.0935-0.4690.27490.2939-0.0335-0.1909-0.38990.29040.12690.63480.0471-0.120.74070.03520.346432.472116.52170.848
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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