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

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Basic information

Entry
Database: PDB / ID: 6lwa
TitleCrystal structure of human NEIL1(P2G, E3Q, K242) 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


: / 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 ...: / 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: 2.76 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)123,5449
Polymers123,5449
Non-polymers00
Water2,486138
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)41,1813
Polymers41,1813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-13 kcal/mol
Surface area15990 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)41,1813
Polymers41,1813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-14 kcal/mol
Surface area16130 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)41,1813
Polymers41,1813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-11 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.559, 109.771, 169.173
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*(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 / Details: Complementary strand / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 55.5 %
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: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 35964 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.06 / Rrim(I) all: 0.151 / Χ2: 1.176 / Net I/σ(I): 5.2 / Num. measured all: 230400
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.860.7817950.8370.3470.8550.506100
2.8-2.856.30.62617540.8440.2720.6830.549100
2.85-2.96.70.53217430.9160.2190.5760.583100
2.9-2.966.80.44417880.9250.1820.480.636100
2.96-3.036.80.40517630.9310.1650.4380.694100
3.03-3.16.70.34317790.9410.1410.3710.76100
3.1-3.176.60.28417670.9550.1180.3080.907100
3.17-3.266.50.2517680.9640.1050.2721.03100
3.26-3.366.30.22817980.9650.0980.2481.037100
3.36-3.4660.21317720.9690.0950.2331.37199.9
3.46-3.596.40.18317750.9780.0780.1991.31699.9
3.59-3.736.70.1717910.980.0710.1841.5899.9
3.73-3.96.60.15417950.9830.0640.1671.6199.9
3.9-4.116.60.13617970.9840.0570.1481.626100
4.11-4.366.30.12618090.9830.0550.1381.686100
4.36-4.75.90.11917920.9830.0540.1311.626100
4.7-5.176.70.11618120.9860.0480.1251.44100
5.17-5.926.50.1118360.9910.0460.1191.537100
5.92-7.465.90.10418620.9870.0470.1151.54499.9
7.46-505.80.08719680.9910.040.0971.51199.8

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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: 2.76→49.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 26.962 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.786 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1765 4.9 %RANDOM
Rwork0.2075 ---
obs0.2095 34141 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 187.89 Å2 / Biso mean: 81.026 Å2 / Biso min: 31.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0 Å2-0 Å2
2---4.11 Å20 Å2
3---5.98 Å2
Refinement stepCycle: final / Resolution: 2.76→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 1575 0 138 7504
Biso mean---61.99 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127697
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186370
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.54210704
X-RAY DIFFRACTIONr_angle_other_deg1.3511.78114661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6575746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11220.029346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52915911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3231564
X-RAY DIFFRACTIONr_chiral_restr0.0790.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027805
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021904
LS refinement shellResolution: 2.76→2.83 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 119 -
Rwork0.296 2378 -
obs--94.37 %
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)
13.22012.14180.00876.5059-1.93831.9194-0.17660.1309-0.0682-0.35810.25160.5759-0.0306-0.0525-0.07490.05320.0093-0.06560.0437-0.01140.12748.616118.413204.539
211.1561-1.97042.14931.5881-0.32991.7560.41790.9150.0799-0.7336-0.26130.06860.1757-0.3203-0.15660.5109-0.0021-0.14150.35420.0320.34951.097125.221188.404
35.9516-1.02440.22999.5041-2.68525.75840.095-0.19410.259-0.52410.1620.0796-0.39990.3971-0.2570.3976-0.0659-0.32070.3775-0.00430.4398-3.897127.839189.025
44.8722-2.1714-0.5064.25830.99873.6141-0.1574-0.23650.36560.29050.1855-0.0724-0.16270.2104-0.02810.09150.0485-0.01450.1036-0.00590.039329.59101.54220.111
511.26092.41611.8333.2834-0.86191.661-0.0612-0.6134-0.1050.3760.18180.00480.40830.0182-0.12060.5750.0766-0.05730.5313-0.05260.241435.9891.8234.851
68.3020.6887-3.55816.69980.2213.7936-0.0961-0.65590.54960.94720.53180.55130.48280.2132-0.43580.41190.2018-0.21590.3974-0.10290.368440.64593.814237.179
75.6155-1.47153.14171.9053-0.97035.6642-0.0154-0.1561-0.17580.0039-0.0882-0.0167-0.10850.47780.10360.93180.12010.04860.63540.17160.274842.71599.883172.98
811.6178-0.933-3.82460.87550.73353.5420.05310.01820.5988-0.2123-0.0174-0.1111-0.1790.0693-0.03570.79630.01170.03530.7819-0.0430.487136.877115.831168.068
98.978-1.49950.58655.9673.64733.3981-0.112-0.09290.28540.3145-0.0488-0.0781-0.3840.05620.16080.68490.0776-0.0620.59240.07410.33632.365117.143170.536
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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