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- PDB-7ayz: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -
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Basic information
Entry | Database: PDB / ID: 7ayz | ||||||
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Title | Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with activator TH10785 | ||||||
![]() | N-glycosylase/DNA lyase | ||||||
![]() | DNA BINDING PROTEIN / 8-oxoguanine DNA glycosylase / N-glycosylase / DNA lyase / DNA repair | ||||||
Function / homology | ![]() 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 / base-excision repair, AP site formation / 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 / base-excision repair, AP site formation / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / cellular response to cadmium ion / response to light stimulus / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / cellular response to reactive oxygen species / response to radiation / base-excision repair / nuclear matrix / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / negative regulation of apoptotic process / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuyer, G. / Davies, J.R. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function. Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / ...Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / Visnes, T. / Sastre-Perona, A. / Danda, A.N. / Homan, E.J. / Marimuthu, K. / Zhenjun, Z. / Chi, C.N. / Sarno, A. / Wiita, E. / von Nicolai, C. / Komor, A.J. / Rajagopal, V. / Muller, S. / Hank, E.C. / Varga, M. / Scaletti, E.R. / Pandey, M. / Karsten, S. / Haslene-Hox, H. / Loevenich, S. / Marttila, P. / Rasti, A. / Mamonov, K. / Ortis, F. / Schomberg, F. / Loseva, O. / Stewart, J. / D'Arcy-Evans, N. / Koolmeister, T. / Henriksson, M. / Michel, D. / de Ory, A. / Acero, L. / Calvete, O. / Scobie, M. / Hertweck, C. / Vilotijevic, I. / Kalderen, C. / Osorio, A. / Perona, R. / Stolz, A. / Stenmark, P. / Berglund, U.W. / de Vega, M. / Helleday, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ayyC ![]() 7az0C ![]() 6g3yS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35816.652 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Truncated mouse OGG1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase #2: Chemical | #3: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.06 M Divalents, 0.1 M Buffer System 3 pH 8.5, 30 % v/v Precipitant Mix 2 (Morpheus screen, Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→85.3 Å / Num. obs: 35633 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4269 / CC1/2: 0.87 / Rpim(I) all: 0.412 / Rrim(I) all: 1.07 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6G3Y Resolution: 2.6→73.873 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.839 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R: 0.897 / ESU R Free: 0.358 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.594 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→73.873 Å
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Refine LS restraints |
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LS refinement shell |
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