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Yorodumi- PDB-5f0s: Crystal structure of C-terminal domain of the human DNA primase l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f0s | ||||||||||||
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Title | Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion | ||||||||||||
Components |
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Keywords | Replication/DNA/RNA / Tranferase-DNA-RNA complex / DNA primase / large subunit / iron-sulfur cluster / RNA / DNA / primer / template / triphosphate / initiation site / manganese / Replication-DNA-RNA complex | ||||||||||||
Function / homology | Function and homology information positive regulation of DNA primase activity / 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 / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere ...positive regulation of DNA primase activity / 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 / 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 / DNA binding / nucleoplasm / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||
Authors | Tahirov, T.H. / Baranovskiy, A.G. / Babayeva, N.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2016 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0s.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0s.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 5f0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0s ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0s | HTTPS FTP |
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-Related structure data
Related structure data | 5exrC 5f0qSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | trimer according to electrophoresis |
-Components
#1: Protein | Mass: 22027.273 Da / Num. of mol.: 2 / Fragment: UNP residues 266-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Escherichia coli (E. coli) References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: RNA chain | Mass: 2106.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: contains 5'-triphosphate / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 3616.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % Description: needle-like prisms with a square in cross-section |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Reservoir solution containe 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride. To ...Details: Reservoir solution containe 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride. To exchange Mg to Mn crystals were soaked for 5 min in a reservoir solution containing 2 mM manganese chloride instead of magnesium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 11834 / % possible obs: 89.9 % / Observed criterion σ(I): -1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.8 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F0Q Resolution: 3→19.87 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4333058 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 13.6132 Å2 / ksol: 0.2824 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.71 Å2 / Biso mean: 52.5 Å2 / Biso min: 4.15 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 3→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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