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- PDB-6r4s: Crystal structure of the Pri1 subunit of human primase bound to ATP -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r4s | ||||||
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Title | Crystal structure of the Pri1 subunit of human primase bound to ATP | ||||||
![]() | DNA primase small subunit | ||||||
![]() | REPLICATION / Primase / DNA-dependent RNA polymerase / ATP / priming | ||||||
Function / homology | ![]() DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / DNA primase activity / Removal of the Flap Intermediate ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / DNA primase activity / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / magnesium ion binding / zinc ion binding / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kilkenny, M.L. / Pellegrini, L. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 484.9 KB | Display | ![]() |
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PDB format | ![]() | 391.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r4tC ![]() 6r4uC ![]() 6r5dC ![]() 6r5eC ![]() 6rb4SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48720.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RB4 Resolution: 2.75→29.32 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.75→29.32 Å
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