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Yorodumi- PDB-4q8f: Human DNA polymerase eta extending primer immediately after a phe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q8f | ||||||
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Title | Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G | ||||||
Components |
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Keywords | TRANSFERASE/DNA / polymerase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å | ||||||
Authors | Gregory, M.T. / Yang, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Authors: Gregory, M.T. / Park, G.Y. / Johnstone, T.C. / Lee, Y.S. / Yang, W. / Lippard, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q8f.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q8f.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 4q8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q8f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4q8f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4q8f_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4q8f_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/4q8f ftp://data.pdbj.org/pub/pdb/validation_reports/q8/4q8f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, POLH RAD30 RAD30A XPV, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y253, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3699.515 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthesized by Sigma-Aldrich and adducted with phenanthriplatin |
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#3: DNA chain | Mass: 2466.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by Sigma-Aldrich |
-Non-polymers , 4 types, 46 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000-MME, MES, pH 6.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.797→30 Å / Num. obs: 11236 / % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.797→29.55 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 23.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Displacement parameters | Biso max: 87.93 Å2 / Biso mean: 35.893 Å2 / Biso min: 11.79 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.797→29.55 Å
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