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Yorodumi- PDB-3e0j: X-ray structure of the complex of regulatory subunits of human DN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e0j | ||||||
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Title | X-ray structure of the complex of regulatory subunits of human DNA polymerase delta | ||||||
Components |
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Keywords | TRANSFERASE / DNA Polymerase Delta / p66 subunit / p50 subunit / human / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / Nucleus / Polymorphism / Phosphoprotein | ||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / nucleotide-excision repair, DNA gap filling / DNA strand elongation involved in DNA replication / DNA biosynthetic process / DNA synthesis involved in DNA repair / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / error-prone translesion synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein-macromolecule adaptor activity / DNA replication / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 3 Å | ||||||
Authors | Baranovskiy, A.G. / Babayeva, N.D. / Pavlov, Y.I. / Vassylyev, D.G. / Tahirov, T.H. | ||||||
Citation | Journal: Cell Cycle / Year: 2008 Title: X-ray structure of the complex of regulatory subunits of human DNA polymerase delta. Authors: Baranovskiy, A.G. / Babayeva, N.D. / Liston, V.G. / Rogozin, I.B. / Koonin, E.V. / Pavlov, Y.I. / Vassylyev, D.G. / Tahirov, T.H. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary crystallographic analysis of the complex of the second and third regulatory subunits of human Pol delta. Authors: Baranovskiy, A.G. / Babayeva, N.D. / Pavlov, Y.I. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e0j.cif.gz | 420.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0j.ent.gz | 353.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e0j_validation.pdf.gz | 511.8 KB | Display | wwPDB validaton report |
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Full document | 3e0j_full_validation.pdf.gz | 653.6 KB | Display | |
Data in XML | 3e0j_validation.xml.gz | 93.6 KB | Display | |
Data in CIF | 3e0j_validation.cif.gz | 125 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0j ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 52224.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P49005, DNA-directed DNA polymerase #2: Protein | Mass: 16233.576 Da / Num. of mol.: 4 / Fragment: residues 1-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q15054 #3: 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: 4.27 Å3/Da / Density % sol: 71.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM imidazole, pH 6.5, 450 mM sodium acetate, 5 mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and 1%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 31, 2007 / Details: Osmic VariMaxTM HR mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 85645 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 8304 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3→29.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3380250.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: fourfold ncs restrained
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.0811 Å2 / ksol: 0.316466 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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