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Yorodumi- PDB-7t5h: Structure of rabies virus phosphoprotein C-terminal domain, wild type -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t5h | |||||||||
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Title | Structure of rabies virus phosphoprotein C-terminal domain, wild type | |||||||||
Components | Phosphoprotein | |||||||||
Keywords | VIRAL PROTEIN / rabies / phosphoprotein / virus / lyssavirus | |||||||||
Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / host cell nucleus Similarity search - Function | |||||||||
Biological species | Rabies virus Nishigahara RCEH | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Zhan, J. / Metcalfe, R.D. / Gooley, P.R. / Griffin, M.D.W. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J.Virol. / Year: 2022 Title: Molecular Basis of Functional Effects of Phosphorylation of the C-Terminal Domain of the Rabies Virus P Protein. Authors: Zhan, J. / Watts, E. / Brice, A.M. / Metcalfe, R.D. / Rozario, A.M. / Sethi, A. / Yan, F. / Bell, T.D.M. / Griffin, M.D.W. / Moseley, G.W. / Gooley, P.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t5h.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5h.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 7t5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t5h_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 7t5h_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 7t5h_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 7t5h_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5h ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5h | HTTPS FTP |
-Related structure data
Related structure data | 7t5gC 1vyiS S: Starting model for refinement 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: 13018.811 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: C297S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rabies virus Nishigahara RCEH / Strain: Nishigahara RCEH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9IPJ8 | ||||||
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#2: Chemical | ChemComp-EDO / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.75 Details: 1.9 M ammonium sulfate, 0.2 M potassium sodium tartrate and 0.1 M sodium citrate (pH 4.75) |
-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: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.99 Å / Num. obs: 18982 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.463 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 928 / CC1/2: 0.816 / Rpim(I) all: 0.411 / Rrim(I) all: 1.544 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vyi Resolution: 1.5→34.83 Å / SU ML: 0.1384 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 22.9442 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 32.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.83 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.205659003875 Å / Origin y: -9.76543998279 Å / Origin z: 11.4348981287 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 190 through 297) |