[English] 日本語
Yorodumi- PDB-7xt0: Crystal structure of RNA helicase from Saint Louis encephalitis v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xt0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of RNA helicase from Saint Louis encephalitis virus and discovery of its inhibitors | ||||||
Components | RNA helicase | ||||||
Keywords | HYDROLASE / St. Louis encephalitis virus / NS3 helicase / crystal structural / virtual screening / inhibitors | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Saint Louis encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Wang, D.P. / Jiang, F.Y. / Zeng, X.Y. / Zhao, R. / Chen, C. / Zhu, Y. / Cao, J.M. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of RNA helicase from Saint Louis encephalitis virus and discovery of its inhibitors Authors: Wang, D.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xt0.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xt0.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xt0_validation.pdf.gz | 918.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xt0_full_validation.pdf.gz | 923.4 KB | Display | |
Data in XML | 7xt0_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7xt0_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xt0 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xt0 | HTTPS FTP |
-Related structure data
Related structure data | 2v8oS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50153.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saint Louis encephalitis virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M5UNY4 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: magnesium chloride hexahydrate, Hepes, pH 7.0, PEG 3350, nickel chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. obs: 38975 / % possible obs: 84.8 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.48→2.57 Å / Rmerge(I) obs: 0.113 / Num. unique obs: 16033 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V8O Resolution: 2.48→43.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.062 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.843 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.64 Å2 / Biso mean: 57.458 Å2 / Biso min: 27.77 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→43.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.48→2.541 Å / Rfactor Rfree error: 0
|