[English] 日本語
Yorodumi- PDB-4ztu: Structural basis for processivity and antiviral drug toxicity in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ztu | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase | ||||||
Components |
| ||||||
Keywords | DNA Binding Protein/DNA / mitochondria / DNA polymerase holoenzyme / DNA Binding Protein-DNA complex | ||||||
Function / homology | Function and homology information gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication proofreading / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication proofreading / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / DNA polymerase binding / 3'-5' exonuclease activity / base-excision repair, gap-filling / Transcriptional activation of mitochondrial biogenesis / base-excision repair / DNA-templated DNA replication / double-stranded DNA binding / protease binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / mitochondrion / DNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.299 Å | ||||||
Authors | Szymanski, M.R. / Kuznestov, V.B. / Shumate, C.K. / Meng, Q. / Lee, Y.-S. / Patel, G. / Patel, S.S. / Yin, Y.W. | ||||||
Citation | Journal: EMBO J. / Year: 2015 Title: Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Authors: Szymanski, M.R. / Kuznestov, V.B. / Shumate, C.K. / Meng, Q. / Lee, Y.-S. / Patel, G. / Patel, S.S. / Yin, Y.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ztu.cif.gz | 391.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ztu.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ztu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ztu_validation.pdf.gz | 789 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ztu_full_validation.pdf.gz | 842.7 KB | Display | |
Data in XML | 4ztu_validation.xml.gz | 63.3 KB | Display | |
Data in CIF | 4ztu_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4ztu ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4ztu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA polymerase subunit gamma- ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 138037.703 Da / Num. of mol.: 1 / Fragment: UNP residues 30-1239 / Mutation: D198A, E200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLG, MDP1, POLG1, POLGA Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P54098, DNA-directed DNA polymerase |
---|---|
#2: Protein | Mass: 53655.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9UHN1 |
-DNA chain , 2 types, 2 molecules TP
#3: DNA chain | Mass: 8235.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#4: DNA chain | Mass: 7421.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 3 molecules
#5: Chemical | #6: Chemical | ChemComp-DCT / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.76 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG8000, KCl, CaCl2 / PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979,1.00 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 3.299→48.6 Å / Num. obs: 61142 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.299→42.67 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.66 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.299→42.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|