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

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Basic information

Entry
Database: PDB / ID: 6lwg
TitleCrystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing guanidinohydantoin (Gh)
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)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: 2.53 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*(DGH)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*(DGH)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*(DGH)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)123,99112
Polymers123,7159
Non-polymers2763
Water5,242291
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)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)41,3304
Polymers41,2383
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-16 kcal/mol
Surface area16070 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)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)41,4235
Polymers41,2383
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-15 kcal/mol
Surface area15940 Å2
MethodPISA
3
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)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)41,2383
Polymers41,2383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-12 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.802, 109.253, 168.249
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*(DGH)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3933.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Oligo DNA containing Gh / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
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: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.53→91.64 Å / Num. obs: 46433 / % possible obs: 99.3 % / Redundancy: 7 % / Rrim(I) all: 0.081 / Net I/σ(I): 19.1
Reflection shellResolution: 2.53→2.59 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3198 / Rrim(I) all: 1.304 / % possible all: 94.5

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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: 2.53→29.69 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 19.914 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 2325 5 %RANDOM
Rwork0.2075 ---
obs0.2098 43731 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.44 Å2 / Biso mean: 73.162 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å2-0 Å2
2---2.79 Å20 Å2
3---4.59 Å2
Refinement stepCycle: final / Resolution: 2.53→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5628 1581 18 291 7518
Biso mean--86.8 62.22 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127545
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186265
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.5410488
X-RAY DIFFRACTIONr_angle_other_deg1.3341.78614395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4035721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41219.707341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98415894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6721566
X-RAY DIFFRACTIONr_chiral_restr0.0780.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021890
LS refinement shellResolution: 2.53→2.592 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.424 151 -
Rwork0.359 3038 -
obs--94.21 %
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)
12.69491.94220.24175.53671.31561.2643-0.15650.16150.0337-0.30040.235-0.4743-0.0450.0827-0.07840.04340.00810.05440.03370.01820.1056-8.384-8.34735.216
28.6638-0.715-2.13811.51080.13123.01450.34791.153-0.342-0.6627-0.2691-0.1446-0.12220.2722-0.07880.46550.00330.14690.3769-0.0470.3632-1.208-15.05919.213
35.8648-1.3211-0.16167.98611.95493.92650.2506-0.0767-0.2158-0.41060.0750.05470.2773-0.3358-0.32570.5035-0.04940.2730.42530.02120.42133.89-17.68319.663
44.662-2.1421-0.04293.6156-0.43043.1527-0.1496-0.2008-0.30270.23950.14510.07870.1259-0.09010.00450.09830.02510.02480.0683-0.00580.0364-29.5638.63150.774
58.03160.3564-2.39384.40381.10714.468-0.1171-0.83730.35950.54470.11620.3585-0.3291-0.09930.00090.34870.09690.00130.45220.01070.1458-35.92117.75565.35
69.77310.20581.17764.287-0.252310.1011-0.1483-0.9997-0.39120.84040.198-0.281-0.0171-0.1761-0.04970.37290.17130.13680.39510.08520.2087-40.56815.867.7
75.462-1.0524-2.73522.18331.30024.64630.1588-0.18680.2892-0.0671-0.13440.03370.0811-0.34-0.02440.79320.1398-0.05030.5995-0.1190.1971-42.0219.4963.921
87.48520.75520.63262.31080.84655.19060.16390.0513-1.1887-0.36070.02490.240.2114-0.2668-0.18880.8261-0.0224-0.03860.8796-0.05430.4422-37.085-5.569-0.841
98.5072-0.71452.12837.6373-3.79814.6537-0.2704-0.4787-0.1330.2399-0.19130.23210.5951-0.20380.46180.68920.10860.13180.7315-0.0960.3292-32.534-7.091.595
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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