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

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Basic information

Entry
Database: PDB / ID: 6lwk
TitleCrystal structure of human NEIL1(P2G, E3Q, R242) 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity ...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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / 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 / 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: 2.88 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)123,67810
Polymers123,5869
Non-polymers921
Water2,630146
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)41,2874
Polymers41,1953
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-14 kcal/mol
Surface area15770 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)41,1953
Polymers41,1953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 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)41,1953
Polymers41,1953
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-13 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.871, 109.096, 169.323
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*(UDH)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3890.538 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: CGTCCA(UDH)GTCTAC / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 31683 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Χ2: 0.85 / Net I/σ(I): 4.6 / Num. measured all: 195803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.87-2.926.20.68815490.840.2970.7510.4699.1
2.92-2.976.10.61915360.8620.2680.6760.48299.1
2.97-3.0360.53215570.8970.2350.5830.47999.7
3.03-3.095.70.43515400.910.1990.480.51699.5
3.09-3.165.80.34415440.9370.1560.3790.54299.7
3.16-3.236.10.29215750.9530.1280.3190.57299.7
3.23-3.316.40.25915640.9630.110.2820.60799.9
3.31-3.46.30.21815740.970.0930.2370.63399.9
3.4-3.56.30.18615650.9770.080.2030.69999.5
3.5-3.626.30.16515600.980.0710.180.76799.9
3.62-3.746.20.14615760.9820.0640.160.88299.6
3.74-3.896.20.13315780.9850.0580.1450.90299.7
3.89-4.075.80.11815820.9850.0540.130.99299.8
4.07-4.296.10.1115730.9820.0490.121.13299.6
4.29-4.556.60.10616000.9850.0450.1161.217100
4.55-4.916.60.115930.9880.0430.1091.161100
4.91-5.46.50.09516050.9880.040.1031.09100
5.4-6.185.90.09116190.990.0410.11.005100
6.18-7.786.50.08216450.9920.0340.0891.047100
7.78-505.90.07917480.9960.0360.0871.59799.9

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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: 2.88→49.63 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.896 / SU B: 31.086 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1612 5.1 %RANDOM
Rwork0.201 ---
obs0.2029 30016 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.61 Å2 / Biso mean: 84.067 Å2 / Biso min: 28.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å2-0 Å2-0 Å2
2---0.32 Å20 Å2
3---3.19 Å2
Refinement stepCycle: final / Resolution: 2.88→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 1572 6 146 7672
Biso mean--100.27 61.11 -
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127859
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186528
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.54510921
X-RAY DIFFRACTIONr_angle_other_deg1.351.77815042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1345757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10920.027374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04615949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8651571
X-RAY DIFFRACTIONr_chiral_restr0.0830.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021963
LS refinement shellResolution: 2.88→2.951 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 109 -
Rwork0.283 2060 -
obs--93.94 %
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)
12.81492.33090.31216.36491.87781.8744-0.15030.16210.0089-0.20980.2445-0.48350.050.0722-0.09410.0280.00250.05920.02620.03910.2378-8.59-8.64135.479
29.9288-2.3416-3.11971.90870.22452.09890.55561.432-0.1675-0.9887-0.4209-0.15370.07430.1689-0.13470.58010.08410.11840.5894-0.12840.5584-1.24-15.31519.452
34.8428-1.3041-0.76879.64882.68654.90180.09420.0782-0.2102-0.70890.195-0.350.3691-0.1971-0.28920.379-0.00710.3320.48640.00450.56613.762-17.96720.051
45.3687-2.3458-0.02074.5629-0.68694.4047-0.2131-0.1613-0.56020.27620.13820.27770.2684-0.1790.07490.10010.03330.05320.0429-0.0090.2104-29.8438.08251.147
58.29060.0877-2.68455.91941.00434.1735-0.1732-0.95250.16360.75180.07110.2193-0.4756-0.28610.10210.4240.131-0.02530.44340.00980.2399-35.91617.67265.741
67.86391.48861.29784.5512-0.023810.2511-0.17-1.0292-0.54341.03730.21-0.15180.0757-0.0954-0.040.39210.23270.19340.42080.15270.4104-40.56715.58468.023
75.9908-0.4785-3.49251.88110.71736.3020.2044-0.0510.1497-0.1857-0.1843-0.0551-0.2931-0.4305-0.02010.97270.137-0.03470.6306-0.14040.4519-42.25810.0543.48
87.34830.37560.17290.1225-0.56665.4230.14540.0443-1.3601-0.15710.08890.04380.0123-0.0414-0.23430.94910.0262-0.22270.8542-0.04490.8193-37.121-5.873-0.972
98.5015-0.0070.47394.1376-2.93473.2249-0.109-0.3626-0.24160.4113-0.08860.12990.35260.05820.19760.84660.1503-0.00770.7863-0.13290.6318-32.589-7.2041.449
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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