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- PDB-9lnq: The hUNG bound to DNA product embedding 4primer-OCH3-dU -

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Basic information

Entry
Database: PDB / ID: 9lnq
TitleThe hUNG bound to DNA product embedding 4primer-OCH3-dU
Components
  • DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*(KBC)P*AP*TP*CP*TP*T)-3')
  • Uracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN/DNA / uracil DNA glycosylase uridine ribonucleotide DNA damage base excision repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLiu, Y. / Zhou, C. / Zhan, X. / Fan, C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877065 China
National Natural Science Foundation of China (NSFC)82111530210 China
Ministry of Science and Technology (MoST, China)2023YFA0913800 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Uridine Embedded within DNA is Repaired by Uracil DNA Glycosylase via a Mechanism Distinct from That of Ribonuclease H2.
Authors: Fan, C. / Zhan, X. / Guo, F. / Li, Q. / Lu, K. / Shan, X. / Zhou, Y. / Ren, M. / Greenberg, M.M. / Liu, Y. / Zhou, C.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*TP*(KBC)P*AP*TP*CP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')
E: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3186
Polymers31,2493
Non-polymers693
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-33 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 65.339, 98.979
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: DNA chain DNA (5'-D(*TP*GP*TP*(KBC)P*AP*TP*CP*TP*T)-3')


Mass: 2727.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')


Mass: 3070.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Uracil-DNA glycosylase / UDG


Mass: 25450.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13051, uracil-DNA glycosylase
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% polyethylene glycol 4000 (Sigma), 100 mM Hepes buffer (pH 6.5), 10% dioxane, 1 mM DTT

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.74→24.74 Å / Num. obs: 402722 / % possible obs: 92.43 % / Redundancy: 13.1 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 1 / Net I/σ(I): 25.69
Reflection shellResolution: 1.74→1.802 Å / Rmerge(I) obs: 1.236 / Num. unique obs: 44792 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→24.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 2872 4.93 %
Rwork0.1922 55413 -
obs0.1938 58285 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.66 Å2 / Biso mean: 34.1832 Å2 / Biso min: 14.69 Å2
Refinement stepCycle: final / Resolution: 1.74→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 385 2 152 2339
Biso mean--30 33.2 -
Num. residues----242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.34191470.338628683015100
1.77-1.80.34081730.310528313004100
1.8-1.830.2981690.292428222991100
1.83-1.860.27521420.262328693011100
1.86-1.90.25651250.256328753000100
1.9-1.940.32891540.25512733288797
1.97-1.990.3194790.23691434151399
1.99-2.040.23411420.238828863028100
2.04-2.090.271370.229128232960100
2.09-2.160.27771230.228728793002100
2.16-2.220.25341480.207128553003100
2.22-2.30.2447800.20291485156552
2.3-2.40.24241420.209328643006100
2.4-2.510.27031560.216328192975100
2.51-2.640.28391390.213628753014100
2.64-2.80.29331020.22291717181961
2.8-3.020.25151400.210428673007100
3.02-3.320.18981590.191828332992100
3.32-3.80.19751420.16012360250283
3.8-4.780.16861230.132728873010100
4.78-24.740.17821500.16512831298199

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