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Yorodumi- PDB-6fad: SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fad | ||||||
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Title | SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27 | ||||||
Components |
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Keywords | SPLICING / Complex / Phosphorylation / Inhibition | ||||||
Function / homology | Function and homology information : / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated suppression of host mRNA processing / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...: / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated suppression of host mRNA processing / sperm DNA condensation / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / negative regulation of viral genome replication / spliceosomal complex assembly / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of viral genome replication / Replacement of protamines by nucleosomes in the male pronucleus / RNA splicing / chromosome segregation / nuclear matrix / host cell cytoplasm / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / host cell nucleus / regulation of DNA-templated transcription / chromatin / magnesium ion binding / endoplasmic reticulum / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Herpes simplex virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å | ||||||
Authors | Tunnicliffe, R.B. / Levy, C. / Mould, A.P. / Mckenzie, E.A. / Sandri-Goldin, R.M. / Golovanov, A.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mbio / Year: 2019 Title: Molecular Mechanism of SR Protein Kinase 1 Inhibition by the Herpes Virus Protein ICP27. Authors: Tunnicliffe, R.B. / Hu, W.K. / Wu, M.Y. / Levy, C. / Mould, A.P. / McKenzie, E.A. / Sandri-Goldin, R.M. / Golovanov, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fad.cif.gz | 600 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fad.ent.gz | 491.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fad_validation.pdf.gz | 469.7 KB | Display | wwPDB validaton report |
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Full document | 6fad_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | 6fad_validation.xml.gz | 29 KB | Display | |
Data in CIF | 6fad_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/6fad ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fad | HTTPS FTP |
-Related structure data
Related structure data | 1wakS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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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-Components
#1: Protein | Mass: 70118.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Truncated construct SRPK1dNS1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SRPK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RP References: UniProt: Q96SB4, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 1746.006 Da / Num. of mol.: 4 / Fragment: ICP27 residues 137-152 / Source method: obtained synthetically / Source: (synth.) Herpes simplex virus (type 1 / strain 17) / References: UniProt: P36295, UniProt: P10238*PLUS #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.09 M (Sodium nitrate, 0.3 Sodium phosphate, 0.3 M ammonium sulphate), 0.1 M (Sodium HEPES, MOPS) buffer system, 50% v/v GOL_P4K mix [Morpheus HT96 C7, Molecular Dimensions] |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.801→80.21 Å / Num. obs: 60695 / % possible obs: 99.95 % / Observed criterion σ(F): 1.36 / Redundancy: 10.1 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0953 / Rpim(I) all: 0.03136 / Rrim(I) all: 0.1004 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.801→2.901 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.7533 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 5993 / CC1/2: 0.812 / Rpim(I) all: 0.2681 / Rrim(I) all: 0.8004 / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WAK Resolution: 2.801→80.21 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→80.21 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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