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- PDB-4bpu: Crystal structure of human primase in heterodimeric form, compris... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bpu | |||||||||
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Title | Crystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain. | |||||||||
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![]() | TRANSFERASE / DNA-DEPENDENT RNA POLYMERASE | |||||||||
Function / homology | ![]() positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / 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 ...positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / 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 / 4 iron, 4 sulfur cluster binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kilkenny, M.L. / Perera, R.L. / Pellegrini, L. | |||||||||
![]() | ![]() Title: Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering Authors: Kilkenny, M.L. / Longo, M. / Perera, R.L. / Pellegrini, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 471.6 KB | Display | ![]() |
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PDB format | ![]() | 393.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.6 KB | Display | ![]() |
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Full document | ![]() | 498.5 KB | Display | |
Data in XML | ![]() | 43.2 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 50108.023 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Protein | Mass: 29782.174 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Details: 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.96 Å / Num. obs: 52124 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 81.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.7→29.617 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 27.74 / Stereochemistry target values: MLHL Details: THE STRUCTURE WAS REFINED IN PHENIX WITH RIDING HYDROGENS. THE HYDROGENS HAVE BEEN INCLUDED IN THE ENTRY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.617 Å
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Refine LS restraints |
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LS refinement shell |
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