[English] 日本語
Yorodumi- PDB-6r4s: Crystal structure of the Pri1 subunit of human primase bound to ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r4s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Pri1 subunit of human primase bound to ATP | ||||||
Components | DNA primase small subunitPrimase | ||||||
Keywords | REPLICATION / Primase / DNA-dependent RNA polymerase / ATP / priming | ||||||
Function / homology | Function and homology information DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / magnesium ion binding / zinc ion binding / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Kilkenny, M.L. / Pellegrini, L. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Authors: Holzer, S. / Rzechorzek, N.J. / Short, I.R. / Jenkyn-Bedford, M. / Pellegrini, L. / Kilkenny, M.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6r4s.cif.gz | 484.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6r4s.ent.gz | 391.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4s ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4s | HTTPS FTP |
---|
-Related structure data
Related structure data | 6r4tC 6r4uC 6r5dC 6r5eC 6rb4SC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48720.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97898 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97898 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→29.32 Å / Num. obs: 25616 / % possible obs: 96.8 % / Redundancy: 4.95 % / CC1/2: 0.984 / Rrim(I) all: 0.177 / Net I/σ(I): 5.46 |
Reflection shell | Resolution: 2.75→2.91 Å / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3730 / CC1/2: 0.36 / Rrim(I) all: 0.917 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RB4 Resolution: 2.75→29.32 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→29.32 Å
|