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Yorodumi- PDB-8vfa: Ternary DNA Polymerase Beta bound to DNA containing primer termin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vfa | ||||||
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Title | Ternary DNA Polymerase Beta bound to DNA containing primer terminal dC base-paired with FapydG | ||||||
Components |
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Keywords | DNA 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 / salivary gland morphogenesis / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision 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 / salivary gland morphogenesis / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Oden, P.N. / Ryan, B.J. / Freudenthal, B.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vfa.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vfa.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vfa_validation.pdf.gz | 784.7 KB | Display | wwPDB validaton report |
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Full document | 8vfa_full_validation.pdf.gz | 794.4 KB | Display | |
Data in XML | 8vfa_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 8vfa_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/8vfa ftp://data.pdbj.org/pub/pdb/validation_reports/vf/8vfa | HTTPS FTP |
-Related structure data
Related structure data | 8vf8C 8vf9C 8vfbC 8vfcC 8vfdC 8vfeC 8vffC 8vfgC 8vfhC 8vfiC 8vfjC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4847.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#4: Protein | 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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-Non-polymers , 4 types, 96 molecules
#5: Chemical | ChemComp-G2P / | ||||
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#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 14-22% PEG 3350 0.05 M Imidazole pH 8.0 0.35 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: May 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→25 Å / Num. obs: 38424 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 24.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.05→2.09 Å / Num. unique obs: 1274 / CC1/2: 0.828 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→24.94 Å / SU ML: 0.2732 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0828 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→24.94 Å
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Refine LS restraints |
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LS refinement shell |
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