[English] 日本語
Yorodumi- PDB-4dl3: Human DNA polymerase eta inserting dCMPNPP opposite GG template (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dl3 | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA polymerase eta inserting dCMPNPP opposite GG template (GG0b). | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/DNA/INHIBITOR / cisplatin / chemoresistence / translesion synthesis / human DNA polymerse eta / kinetics / molecular splint / inhibition / DNA distorsion / second TLS polymerase / nucleotidyl transfer reaction / PCNA / nucleus / TRANSFERASE-DNA-INHIBITOR 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhao, Y. / Biertumpfel, C. / Gregory, M. / Hua, Y. / Hanaoka, F. / Yang, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Authors: Zhao, Y. / Biertumpfel, C. / Gregory, M.T. / Hua, Y.J. / Hanaoka, F. / Yang, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dl3.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dl3.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dl3_validation.pdf.gz | 813.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dl3_full_validation.pdf.gz | 829.5 KB | Display | |
Data in XML | 4dl3_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 4dl3_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/4dl3 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/4dl3 | HTTPS FTP |
-Related structure data
Related structure data | 4dl2C 4dl4C 4dl5C 4dl6C 4dl7C 3mr2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: unp residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9Y253, DNA-directed DNA polymerase |
---|
-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3622.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cisplatin-crosslinked oligonucleotide, chain T |
---|---|
#3: DNA chain | Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide, chain P |
-Non-polymers , 4 types, 283 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-0KX / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.97 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 6 Details: MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2010 Details: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING |
Radiation | Monochromator: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 25209 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.71 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.096 / Net I/σ(I): 12.73 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.47 / Rsym value: 0.576 / % possible all: 97.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MR2 Resolution: 2.1→30 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.59 / σ(F): 1.34 / Phase error: 21.37 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.49 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|