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Yorodumi- PDB-5yvu: Crystal structures of unlinked full length NS3 from Dengue virus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yvu | |||||||||||||||
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Title | Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain | |||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / FLAVIVIRUS / DENGUE | |||||||||||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / 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 / serine protease inhibitor complex / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / serine-type endopeptidase inhibitor activity / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / protease binding / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / calcium ion binding / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular space / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Dengue virus 4 Bos taurus (cattle) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å | |||||||||||||||
Authors | Phoo, W.W. / El Sahili, A. | |||||||||||||||
Funding support | Singapore, 4items
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Citation | Journal: To Be Published Title: Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain Authors: Phoo, W.W. / El Sahili, A. / ZHANG, Z.Z. / CHEN, M.W. / VASUDEVAN, S. / LESCAR, J. / LUO, D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yvu.cif.gz | 287.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yvu.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yvu ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yvu | HTTPS FTP |
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-Related structure data
Related structure data | 5yvjC 5yvvC 5yvwC 5yvyC 5yw1C 2vbcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70044.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1475-2092 / Mutation: S135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4 |
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#2: Protein | Mass: 5964.470 Da / Num. of mol.: 1 / Fragment: UNP residues 1393-1439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4 |
#3: Protein | Mass: 6342.387 Da / Num. of mol.: 1 / Fragment: UNP residues 36-90 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974 |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.4, 12% PEG6000 / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.491→47.7 Å / Num. obs: 50500 / % possible obs: 94.85 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.42 Å2 / CC1/2: 0.917 / Rmerge(I) obs: 0.1176 / Rrim(I) all: 0.1389 / Net I/σ(I): 14.03 |
Reflection shell | Resolution: 2.491→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5446 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 2458 / CC1/2: 0.799 / Rrim(I) all: 0.1389 / % possible all: 92.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VBC Resolution: 2.491→47.704 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 30.2 / 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: 2.491→47.704 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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