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- PDB-6m7t: Human DNA polymerase eta in a non-productive ternary complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m7t | ||||||
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Title | Human DNA polymerase eta in a non-productive ternary complex with Ca2+ and dTTP oppositing cdA | ||||||
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![]() | TRANSFERASE/DNA / TRANSLESION SYNTHESIS / cdA / DNA BINDING PROTEIN / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / 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 / error-prone translesion synthesis / regulation of DNA repair / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weng, P. / Gao, Y. / Yang, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution. Authors: Weng, P.J. / Gao, Y. / Gregory, M.T. / Wang, P. / Wang, Y. / Yang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.5 KB | Display | ![]() |
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PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.4 KB | Display | ![]() |
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Full document | ![]() | 787.9 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m7oC ![]() 6m7pC ![]() 6m7uC ![]() 6m7vC ![]() 3si8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 / Fragment: residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 3275.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 6 types, 40 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NI / | ||
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#5: Chemical | ChemComp-TTP / | ||
#6: Chemical | ChemComp-CA / | ||
#7: Chemical | ChemComp-EDO / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 16 % PEG 2000 MME 100 mM MES, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 19880 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.643 / Num. unique obs: 1364 / CC1/2: 0.894 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SI8 Resolution: 2.8→29.734 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 29.84 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.734 Å
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Refine LS restraints |
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LS refinement shell |
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