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- PDB-9nz9: Crystal structure of product-bound human OGG1(WT) -

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Basic information

Entry
Database: PDB / ID: 9nz9
TitleCrystal structure of product-bound human OGG1(WT)
Components
  • DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*T)-3')
  • DNA (5'-D(P*AP*CP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*AP*GP*AP*GP*TP*CP*(PUA))-3')
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / LYASE/DNA / DNA-glycosylase / AP-lyase / LYASE-DNA complex
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / 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 / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / 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 / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / endonuclease activity / response to oxidative stress / microtubule binding / damaged DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / 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 / cytosol
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
DNA / DNA (> 10) / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSyed, A. / Arvai, A.S. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
CitationJournal: Nat Commun / Year: 2026
Title: A unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.
Authors: Syed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. / Tsai, C.L. / Bacolla, A. / Shin, D.S. / Cunningham, ...Authors: Syed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. / Tsai, C.L. / Bacolla, A. / Shin, D.S. / Cunningham, R.P. / Iwai, S. / Chowdhury, D. / Lloyd, R.S. / Ivanov, I. / Tainer, J.A.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
C: DNA (5'-D(P*TP*AP*GP*AP*GP*TP*CP*(PUA))-3')
B: DNA (5'-D(P*AP*CP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9375
Polymers44,8744
Non-polymers621
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-13 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.543, 91.543, 213.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-glycosylase/DNA lyase


Mass: 35891.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli (E. coli)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 3 types, 3 molecules CBD

#2: DNA chain DNA (5'-D(P*TP*AP*GP*AP*GP*TP*CP*(PUA))-3')


Mass: 2315.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*TP*GP*C)-3')


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*T)-3')


Mass: 4584.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 125 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 16-23% PEG6000, cryoprotectant: 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2→213.39 Å / Num. obs: 36687 / % possible obs: 99.9 % / Redundancy: 19.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 14
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2592 / CC1/2: 0.421 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→74.32 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1619 5.02 %
Rwork0.1853 --
obs0.1882 32265 88.12 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→74.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 557 4 124 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093194
X-RAY DIFFRACTIONf_angle_d1.0024454
X-RAY DIFFRACTIONf_dihedral_angle_d22.961210
X-RAY DIFFRACTIONf_chiral_restr0.057483
X-RAY DIFFRACTIONf_plane_restr0.01485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.37021020.35551888X-RAY DIFFRACTION67
2.06-2.130.40631120.31152076X-RAY DIFFRACTION73
2.13-2.20.37661120.29052162X-RAY DIFFRACTION76
2.2-2.290.32471200.25592289X-RAY DIFFRACTION80
2.29-2.390.27221290.22052457X-RAY DIFFRACTION86
2.39-2.520.28191400.19732549X-RAY DIFFRACTION90
2.52-2.680.23971410.18722638X-RAY DIFFRACTION92
2.68-2.880.29141410.22062765X-RAY DIFFRACTION96
2.88-3.170.26341470.20372817X-RAY DIFFRACTION97
3.17-3.630.23481500.19082892X-RAY DIFFRACTION99
3.63-4.580.2011560.15332968X-RAY DIFFRACTION99
4.58-74.320.22171690.15893145X-RAY DIFFRACTION99

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