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- PDB-4bpx: Crystal structure of human primase in complex with the primase- b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bpx | |||||||||
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Title | Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha | |||||||||
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![]() | TRANSFERASE / DNA REPLICATION / FUSION PROTEIN / CHIMERA | |||||||||
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 / regulation of type I interferon production / Polymerase switching ...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 / regulation of type I interferon production / 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 / primosome complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol 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 | ![]() | 459.4 KB | Display | ![]() |
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PDB format | ![]() | 381.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bpuSC ![]() 4bpwC S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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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: 30774.051 Da / Num. of mol.: 2 Fragment: PRIMASE-BINDING MOTIF RESIDUES 1445-1462, PRIL RESIDUES 19-253 Source method: isolated from a genetically manipulated source Details: PRIL IS FUSED AT THE N-TERMINUS TO THE PRIMASE-BINDING MOTIF OF DNA POLYMERASE ALPHA (CHAIN E), VIA A 15-AMINO ACID LINKER OF SEQUENCE TGSTGSTGSTGSTGS Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P09884, UniProt: P49643, DNA-directed DNA polymerase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #3: Chemical | Sequence details | CHAINS B AND D ARE ENGINEERED, CHIMERIC PROTEIN CONSTRUCTS. IN EACH CONSTRUCT, THE AMINO-TO- ...CHAINS B AND D ARE ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68 % / 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 | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→49.37 Å / Num. obs: 28805 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 170.66 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BPU Resolution: 3.4→45.325 Å / SU ML: 0.63 / σ(F): 1.32 / Phase error: 34.39 / Stereochemistry target values: ML 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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 200.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→45.325 Å
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Refine LS restraints |
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LS refinement shell |
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