[English] 日本語
Yorodumi- PDB-2gg1: NMR solution structure of domain III of the E-protein of tick-bor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gg1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | NMR solution structure of domain III of the E-protein of tick-borne Langat flavivirus (includes RDC restraints) | |||||||||
Components | Genome polyprotein | |||||||||
Keywords | VIRAL PROTEIN / Domain III | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Langat virus | |||||||||
Method | SOLUTION NMR / distance geometry simulated annealing | |||||||||
Authors | Mukherjee, M. / Dutta, K. / White, M.A. / Cowburn, D. / Fox, R.O. | |||||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition. Authors: Mukherjee, M. / Dutta, K. / White, M.A. / Cowburn, D. / Fox, R.O. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gg1.cif.gz | 558.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gg1.ent.gz | 460.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gg1_validation.pdf.gz | 412.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2gg1_full_validation.pdf.gz | 581.1 KB | Display | |
Data in XML | 2gg1_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 2gg1_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2gg1 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2gg1 | HTTPS FTP |
-Related structure data
Related structure data | 1z66C C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11176.670 Da / Num. of mol.: 1 / Fragment: Domain III, Major envelope protein E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Langat virus / Genus: Flavivirus / Plasmid: His-MBP-T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 Codon plus / References: UniProt: P29838, UniProt: P29837*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 0.7mM Langat E-protein domain III, U-15N,13C, 20mM Bis-Tris, 10mM NaCl, 95% H2O, 5% D2O Solvent system: 95% H2O/5% D2O |
---|---|
Sample conditions | Ionic strength: 10mM NaCl / pH: 6.2 / Pressure: Ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |