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- PDB-8vff: Binary DNA Polymerase Beta bound to DNA containing primer termina... -

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Basic information

Entry
Database: PDB / ID: 8vff
TitleBinary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(FAP))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsDNA BINDING PROTEIN/DNA / FapydG / Polymerase Beta / primer terminus / Pol Beta / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / in utero embryonic development / microtubule / response to ethanol / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site ...DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsOden, P.N. / Ryan, B.J. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES-027558 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.
Authors: Gao, S. / Oden, P.N. / Ryan, B.J. / Yang, H. / Freudenthal, B.D. / Greenberg, M.M.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(FAP))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7966
Polymers47,7504
Non-polymers462
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-47 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.399, 79.277, 54.885
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(FAP))-3')


Mass: 3119.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 370 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 14-22% PEG 3350 0.05 M Imidazole pH 8.0 0.35 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.69→25 Å / Num. obs: 43590 / % possible obs: 93.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 1.69→1.73 Å / Num. unique obs: 2102 / CC1/2: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→23.64 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2012 4.62 %
Rwork0.2148 41578 -
obs0.2156 43590 86.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.58 Å2
Refinement stepCycle: LAST / Resolution: 1.69→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 635 2 368 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973348
X-RAY DIFFRACTIONf_angle_d1.25064640
X-RAY DIFFRACTIONf_chiral_restr0.0814511
X-RAY DIFFRACTIONf_plane_restr0.0127491
X-RAY DIFFRACTIONf_dihedral_angle_d20.61331301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.2668760.261490X-RAY DIFFRACTION43.98
1.73-1.780.28991070.27522127X-RAY DIFFRACTION61.85
1.78-1.830.27641130.29042397X-RAY DIFFRACTION70.49
1.83-1.890.34291340.29252782X-RAY DIFFRACTION80.87
1.89-1.960.30231440.27833038X-RAY DIFFRACTION89.51
1.96-2.040.24731550.23223172X-RAY DIFFRACTION92.88
2.04-2.130.24091610.23423212X-RAY DIFFRACTION94.48
2.13-2.240.26761580.23053295X-RAY DIFFRACTION96.05
2.24-2.380.27951640.23223333X-RAY DIFFRACTION97.46
2.38-2.560.29781600.23683318X-RAY DIFFRACTION97.04
2.56-2.820.21741570.23613328X-RAY DIFFRACTION96.99
2.82-3.230.21871590.22633342X-RAY DIFFRACTION96.87
3.23-4.060.19171590.17083307X-RAY DIFFRACTION95.8
4.07-23.640.17231650.15983437X-RAY DIFFRACTION98.07

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