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- PDB-5ity: Crystal Structure of Human NEIL1(P2G) bound to duplex DNA contain... -

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Basic information

Entry
Database: PDB / ID: 5ity
TitleCrystal Structure of Human NEIL1(P2G) bound to duplex DNA containing Thymine Glycol
Components
  • DNA (26-MER)
  • Endonuclease 8-like 1
KeywordsDNA BINDING PROTEIN/DNA / DNA glycosylase NEIL1 Fpg Nei base excision 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 / 8-oxo-7,8-dihydroguanine 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 / 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 / 8-oxo-7,8-dihydroguanine 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 / 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, gap-filling / 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 / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / 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 ...Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / 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 / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsZhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y. / Yi, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair
Authors: Zhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y.Q. / Yi, C.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Endonuclease 8-like 1
C: Endonuclease 8-like 1
D: DNA (26-MER)
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7427
Polymers158,6506
Non-polymers921
Water6,485360
1
A: Endonuclease 8-like 1
D: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)52,8832
Polymers52,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-10 kcal/mol
Surface area15580 Å2
MethodPISA
2
B: Endonuclease 8-like 1
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9763
Polymers52,8832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area15610 Å2
MethodPISA
3
C: Endonuclease 8-like 1
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)52,8832
Polymers52,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-7 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.624, 108.706, 169.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 44885.309 Da / Num. of mol.: 3 / Mutation: P2G, K242R
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 (26-MER)


Mass: 7998.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.1M cacodylic acid (pH 7.0), 0.1M NaCl, 0.05M MgCl2, 24%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.48→91.58 Å / Num. obs: 46040 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.055 / Net I/av σ(I): 21.7 / Net I/σ(I): 21.7
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.14 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDH

1tdh


Resolution: 2.48→91.58 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22456 2387 4.9 %RANDOM
Rwork0.17552 ---
obs0.178 46040 98.05 %-
Refinement stepCycle: LAST / Resolution: 2.48→91.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 1581 6 360 8201
LS refinement shellResolution: 2.476→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 149 -
Rwork0.306 3171 -
obs--91.89 %

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