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Yorodumi- PDB-8qxx: HCMV DNA polymerase processivity factor UL44 phosphorylated NLS 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qxx | ||||||
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Title | HCMV DNA polymerase processivity factor UL44 phosphorylated NLS 410-433 bound to mouse importin alpha 2 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / importin / karyopherin / nuclear / nls | ||||||
Function / homology | Function and homology information Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA polymerase processivity factor activity ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA polymerase processivity factor activity / virion component / cytoplasmic stress granule / protein import into nucleus / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA-binding transcription factor binding / DNA replication / postsynaptic density / virus-mediated perturbation of host defense response / glutamatergic synapse / host cell nucleus / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Human betaherpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cross, E.M. / Marin, O. / Ariawan, D. / Aragao, D. / Cozza, G. / Di Iorio, E. / Forwood, J.K. / Alvisi, G. | ||||||
Funding support | 1items
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Citation | Journal: Febs Lett. / Year: 2024 Title: Structural determinants of phosphorylation-dependent nuclear transport of HCMV DNA polymerase processivity factor UL44. Authors: Cross, E.M. / Marin, O. / Ariawan, D. / Aragao, D. / Cozza, G. / Di Iorio, E. / Forwood, J.K. / Alvisi, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qxx.cif.gz | 225.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qxx.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qxx_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 8qxx_full_validation.pdf.gz | 452.1 KB | Display | |
Data in XML | 8qxx_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 8qxx_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qxx ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qxx | HTTPS FTP |
-Related structure data
Related structure data | 8qxwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 |
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#2: Protein/peptide | Mass: 2816.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human betaherpesvirus 5 / References: UniProt: P16790 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate 0.65M, HEPES pH7.0, DTT 0.01M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.39 Å / Num. obs: 55424 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3510 / CC1/2: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.88 Å / SU ML: 0.237 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7769 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 45.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.88 Å
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Refine LS restraints |
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LS refinement shell |
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