+Open data
-Basic information
Entry | Database: PDB / ID: 5xc6 | ||||||
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Title | Dengue Virus 4 NS3 Helicase in complex with SSRNA SLA12 | ||||||
Components |
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Keywords | HYDROLASE/RNA / Helicase / Dengue NS3 / RNA / Hydrolase / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral RNA genome replication / serine-type endopeptidase activity / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 4 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Swarbrick, C.M.D. / Basavannacharya, C. / Chan, K.W.K. / Chan, S.A. / Singh, D. / Wei, N. / Phoo, W.W. / Luo, D. / Lescar, J. / Vasudevan, S.G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication Authors: Swarbrick, C.M.D. / Basavannacharya, C. / Chan, K.W.K. / Chan, S.A. / Singh, D. / Wei, N. / Phoo, W.W. / Luo, D. / Lescar, J. / Vasudevan, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xc6.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xc6.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xc6 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xc6 | HTTPS FTP |
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-Related structure data
Related structure data | 5xc7C 2jluS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51365.527 Da / Num. of mol.: 2 / Fragment: UNP residues 1646-2092 / Mutation: E250D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 4 / Strain: Thailand/0348/1991 / Production host: Escherichia coli (E. coli) / References: UniProt: M9P7S0 #2: RNA chain | Mass: 3791.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 15% polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.86 Å / Num. obs: 19928 / % possible obs: 99.7 % / Redundancy: 3.6 % / Net I/σ(I): 8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JLU Resolution: 2.9→19.859 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.859 Å
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Refine LS restraints |
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LS refinement shell |
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