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- PDB-6w0r: Human 8-oxoguanine glycosylase interrogating fully intrahelical u... -

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Basic information

Entry
Database: PDB / ID: 6w0r
TitleHuman 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA
Components
  • DNA (5'-D(P*CP*AP*GP*GP*TP*C)-3')
  • DNA (5'-D(P*CP*CP*TP*GP*G)-3')
  • N-glycosylase/DNA lyase
KeywordsLyase/DNA / hOGG1 / 8-oxoG / Encounter complex / Interrogation complex / DNA BINDING PROTEIN / 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 / positive regulation of gene expression via chromosomal CpG island demethylation / 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 / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / 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 / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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
NITRATE ION / 2-(2-ethoxyethoxy)ethanethiol / DNA / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsShigdel, U. / Verdine, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2020
Title: The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.
Authors: Shigdel, U.K. / Ovchinnikov, V. / Lee, S.J. / Shih, J.A. / Karplus, M. / Nam, K. / Verdine, G.L.
History
DepositionMar 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: DNA (5'-D(P*CP*AP*GP*GP*TP*C)-3')
C: DNA (5'-D(P*CP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9668
Polymers38,6073
Non-polymers3595
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-21 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.928, 88.928, 210.539
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-glycosylase/DNA lyase


Mass: 35301.965 Da / Num. of mol.: 1 / Mutation: E122Q, Y207C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*CP*CP*TP*GP*G)-3')


Mass: 1496.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 119 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: NO3
#6: Chemical ChemComp-S5Y / 2-(2-ethoxyethoxy)ethanethiol


Mass: 150.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM NH4NO3, and 20 % polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→44.46 Å / Num. obs: 21524 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.3
Reflection shellResolution: 2.35→2.47 Å / Rmerge(I) obs: 0.989 / Num. unique obs: 3060

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
PHASERphasing
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBM

1ebm


Resolution: 2.35→43.5 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1099 5.12 %RANDOM
Rwork0.2084 ---
obs0.2104 21448 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.38 Å2 / Biso mean: 39.7253 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.35→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 225 22 115 2823
Biso mean--54.97 34.08 -
Num. residues----323
LS refinement shellResolution: 2.35→2.4 Å /
RfactorNum. reflection
Rfree0.316 -
Rwork0.285 -
obs-2475
Refinement TLS params.Method: refined / Origin x: 3.137 Å / Origin y: -23.294 Å / Origin z: -1.879 Å
111213212223313233
T0.2278 Å20.0236 Å20.0174 Å2-0.1486 Å20.0166 Å2--0.2292 Å2
L1.1937 °2-0.003 °20.3188 °2-0.0405 °20.1935 °2--1.1035 °2
S0.0417 Å °-0.1076 Å °-0.1688 Å °0.0016 Å °0.004 Å °-0.0396 Å °0.1106 Å °-0.0025 Å °0.0017 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 323
2X-RAY DIFFRACTION1B21 - 26
3X-RAY DIFFRACTION1C6 - 10
4X-RAY DIFFRACTION1A401
5X-RAY DIFFRACTION1B101
6X-RAY DIFFRACTION1A402 - 404
7X-RAY DIFFRACTION1A501 - 611
8X-RAY DIFFRACTION1B201 - 203

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