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- PDB-9nza: Crystal structure of human OGG1 (WT) in a product bound state in ... -

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Basic information

Entry
Database: PDB / ID: 9nza
TitleCrystal structure of human OGG1 (WT) in a product bound state in the presence of the agonist F01
Components
  • (DNA (5'-D(P*AP*CP*CP*TP*GP*CP*A)- ...) x 2
  • DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-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
8-OXOGUANINE / DNA / DNA (> 10) / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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*AP*CP*CP*TP*GP*CP*A)-3')
B: DNA (5'-D(P*AP*CP*CP*TP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0405
Polymers44,8744
Non-polymers1651
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-10 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.176, 91.176, 212.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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DNA (5'-D(P*AP*CP*CP*TP*GP*CP*A)- ... , 2 types, 2 molecules CB

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


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA chain , 2 types, 2 molecules AD

#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
#4: DNA chain DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-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, 35 molecules

#5: Chemical ChemComp-OXG / 8-OXOGUANINE


Mass: 165.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES, pH 6.0, 16-23% PEG6000, 4.5 mM F01, cryoprotectant: 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→39.48 Å / Num. obs: 18911 / % possible obs: 100 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.039 / Rrim(I) all: 1.171 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2078 / CC1/2: 0.301 / % possible all: 100

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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: 2.5→39.48 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 837 4.96 %
Rwork0.2061 --
obs0.2081 16892 89.6 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 557 12 34 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023211
X-RAY DIFFRACTIONf_angle_d0.54482
X-RAY DIFFRACTIONf_dihedral_angle_d20.4341210
X-RAY DIFFRACTIONf_chiral_restr0.036483
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.38861110.38192115X-RAY DIFFRACTION73
2.66-2.860.35271150.31232376X-RAY DIFFRACTION81
2.86-3.150.30511390.28452580X-RAY DIFFRACTION88
3.15-3.60.24821460.23592833X-RAY DIFFRACTION96
3.6-4.540.22491570.18242960X-RAY DIFFRACTION99
4.54-39.480.22221690.17163191X-RAY DIFFRACTION100
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)
10.3482-0.2619-0.28040.60610.37170.2803-0.08310.2798-0.1274-0.1528-0.13720.0496-0.0421-0.5271-00.5457-0.0681-0.01760.6488-0.12650.4953-12.3205-18.9491-5.9285
20.9949-0.13750.20410.72940.12720.74430.061-0.0595-0.0444-0.0857-0.0558-0.0741-0.1975-0.208200.4981-0.13960.04040.4561-0.03030.50543.504-20.65010.3734
31.0034-0.5262-0.23530.50650.19760.0619-0.02320.1091-0.0374-0.44060.2721-0.171-0.170.30100.5565-0.11380.07760.5487-0.10990.602516.057-27.8372-7.3616
40.15910.0221-0.06020.1068-0.180.2633-0.4173-1.0074-0.9921-0.567-0.3306-0.90920.25790.2982-0.00921.041-0.0439-0.10761.03320.09261.398615.747-37.376112.6339
50.1590.0176-0.17020.21050.0010.1359-0.0701-0.0774-2.04640.4653-0.8475-0.37340.71030.1743-0.07381.1316-0.13340.07890.82970.08491.64416.5458-37.194312.4984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 325 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 14 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 14 )

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