+
Open data
-
Basic information
Entry | Database: PDB / ID: 5exr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human primosome | |||||||||
![]() |
| |||||||||
![]() | REPLICATION / human primosome / complex / primase / DNA polymerase alpha / primer / DNA replication / DNA / RNA / replicase | |||||||||
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 / protein import into nucleus / 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 | ![]() ![]() ![]() ![]() | |||||||||
![]() | Tahirov, T.H. / Baranovskiy, A.G. / Babayeva, N.D. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. Authors: Baranovskiy, A.G. / Babayeva, N.D. / Zhang, Y. / Gu, J. / Suwa, Y. / Pavlov, Y.I. / Tahirov, T.H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 956.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 762.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5f0qC ![]() 5f0sC ![]() 4q5vS ![]() 4qclS ![]() 4rr2S ![]() 4y97S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | tetramer according to electrophoresis |
-
Components
-Protein , 2 types, 4 molecules AEBF
#1: Protein | Mass: 49981.012 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: Protein | Mass: 58890.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
---|
-DNA polymerase alpha ... , 2 types, 4 molecules CGDH
#3: Protein | Mass: 129308.773 Da / Num. of mol.: 2 / Mutation: V516A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 65884.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 2 types, 8 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SF4.gif)
#5: Chemical | ChemComp-ZN / #6: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.46 % / Description: thin plate in form of parallelogram |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 74238 / % possible obs: 80.5 % / Observed criterion σ(I): -1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.063 / Χ2: 2.353 / Net I/av σ(I): 8 / Net I/σ(I): 12.2 / Num. measured all: 236349 |
Reflection shell | Resolution: 3.6→3.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.93 / Num. unique all: 3348 / Χ2: 0.764 / Rejects: 0 / % possible all: 72.7 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4QCL, 4Q5V, 4RR2, 4Y97 Resolution: 3.6→39.94 Å / Data cutoff high absF: 6416908 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 161.81 Å2 / ksol: 0.4022 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.71 Å2 / Biso mean: 61.2 Å2 / Biso min: 1.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→39.94 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.6→3.83 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|