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Yorodumi- PDB-2p5p: Crystal Structure Analysis of the West Nile virus envelope (E) pr... -
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-Basic information
Entry | Database: PDB / ID: 2p5p | ||||||
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Title | Crystal Structure Analysis of the West Nile virus envelope (E) protein domain III | ||||||
Components | Genome polyprotein | ||||||
Keywords | VIRAL PROTEIN / West Nile virus / Envelope protein | ||||||
Function / homology | Function and homology information RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication / 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 / protein-DNA complex / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / peptidase activity / 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 / ribonucleoprotein complex / 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 / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | West Nile virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gao, F. / Yuan, F. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of the West Nile virus envelope (E) protein domain III Authors: Liu, J. / Gao, F. / Yuan, F. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p5p.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p5p.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p5p_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 2p5p_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 2p5p_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2p5p_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/2p5p ftp://data.pdbj.org/pub/pdb/validation_reports/p5/2p5p | HTTPS FTP |
-Related structure data
Related structure data | 1ztxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12242.850 Da / Num. of mol.: 3 Fragment: envelope protein domain III, Major envelope protein E, residues 1-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06935 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M ammonium sulfate, 100mM Tris-HCl, 9-10%(v/v) DMSO, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 7787 / Num. obs: 6605 / Redundancy: 8.1 % |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.545 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZTX Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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