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- PDB-8cex: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 8cex
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH11227.
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / protein in complex with fragment inhibitor
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / microtubule binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
NICKEL (II) ION / : / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKosenina, S. / Scaletti, E.R. / Stenmark, P.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Cancerfonden20 1287 PjF Sweden
Swedish Research Council2022-03681 Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Virtual fragment screening for DNA repair inhibitors in vast chemical space.
Authors: Luttens, A. / Vo, D.D. / Scaletti, E.R. / Wiita, E. / Almlof, I. / Wallner, O. / Davies, J. / Kosenina, S. / Meng, L. / Long, M. / Mortusewicz, O. / Masuyer, G. / Ballante, F. / Michel, M. / ...Authors: Luttens, A. / Vo, D.D. / Scaletti, E.R. / Wiita, E. / Almlof, I. / Wallner, O. / Davies, J. / Kosenina, S. / Meng, L. / Long, M. / Mortusewicz, O. / Masuyer, G. / Ballante, F. / Michel, M. / Homan, E. / Scobie, M. / Kalderen, C. / Warpman Berglund, U. / Tarnovskiy, A.V. / Radchenko, D.S. / Moroz, Y.S. / Kihlberg, J. / Stenmark, P. / Helleday, T. / Carlsson, J.
History
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: N-glycosylase/DNA lyase
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7535
Polymers107,4503
Non-polymers3032
Water1,33374
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1203
Polymers35,8171
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase


Theoretical massNumber of molelcules
Total (without water)35,8171
Polymers35,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase


Theoretical massNumber of molelcules
Total (without water)35,8171
Polymers35,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.113, 81.306, 170.254
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 N-glycosylase/DNA lyase


Mass: 35816.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli (E. coli)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-UG0 / 6-fluoranyl-N-[(4-methylphenyl)methyl]pyridine-3-carboxamide


Mass: 244.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG4000, 20% v/v glycerol, 0.03M of each ethylene glycol, 0.1M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.3→58.866 Å / Num. obs: 50891 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.057 / Rrim(I) all: 0.151 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.5 % / Num. unique obs: 4601 / CC1/2: 0.543 / Rrim(I) all: 2.221

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHASERphasing
Aimlessdata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.3→58.866 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.244 / Average fsc free: 0.9381 / Average fsc work: 0.9537 / Cross valid method: FREE R-VALUE / ESU R: 0.362 / ESU R Free: 0.256 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2775 2664 5.243 %
Rwork0.242 48142 -
all0.244 --
obs-50806 99.921 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.516 Å20 Å2-0 Å2
2--0.414 Å2-0 Å2
3---0.102 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7375 0 19 74 7468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127601
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6510344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.982561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.447101196
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.48210360
X-RAY DIFFRACTIONr_chiral_restr0.0690.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025828
X-RAY DIFFRACTIONr_nbd_refined0.230.22824
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2203
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.25
X-RAY DIFFRACTIONr_mcbond_it6.7346.6863700
X-RAY DIFFRACTIONr_mcangle_it9.43410.0034611
X-RAY DIFFRACTIONr_scbond_it6.556.9983901
X-RAY DIFFRACTIONr_scangle_it9.01110.3355733
X-RAY DIFFRACTIONr_lrange_it12.65897.83210778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.3591890.32534960.32736890.920.92799.89160.328
2.36-2.4240.3571720.32934290.3336040.9090.93199.91680.332
2.424-2.4940.361440.28233640.28535110.9310.9599.91460.281
2.494-2.5710.2931900.28332210.28334110.9430.951000.275
2.571-2.6550.3831740.29331360.29733130.9090.94799.90940.283
2.655-2.7480.341530.27330580.27632130.9250.9599.93780.261
2.748-2.8520.3371670.27929230.28330900.9250.9511000.263
2.852-2.9680.3231670.2728230.27329900.9340.9521000.255
2.968-3.0990.3331820.26527140.26928960.9350.9561000.251
3.099-3.250.3251410.28526180.28727590.9260.9491000.273
3.25-3.4250.2751290.26424760.26526050.9540.961000.256
3.425-3.6320.3021250.25523500.25724760.9430.96399.95960.25
3.632-3.8820.2521100.23822460.23923570.9610.96599.95760.237
3.882-4.1920.2771490.22320340.22621830.9490.971000.226
4.192-4.5890.2311030.20919290.21120320.9640.9731000.219
4.589-5.1270.225940.20417550.20518490.970.9731000.216
5.127-5.9130.252970.21415340.21616310.9650.9721000.227
5.913-7.2240.25850.23413290.23514140.9720.9691000.247
7.224-10.140.198600.18110640.18211240.9720.981000.208
10.14-58.8660.283330.2286430.236780.9480.96299.7050.271

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