+Open data
-Basic information
Entry | Database: PDB / ID: 2jlr | ||||||
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Title | Dengue virus 4 NS3 helicase in complex with AMPPNP | ||||||
Components | SERINE PROTEASE SUBUNIT NS3 | ||||||
Keywords | HYDROLASE / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / HELICASE / PROTEASE / ATP ANALOG / TRANSFERASE / VIRAL NUCLEOPROTEIN / ENDOPLASMIC RETICULUM / CLEAVAGE ON PAIR OF BASIC RESIDUES / MULTIFUNCTIONAL ENZYME / TRANSCRIPTION REGULATION / NUCLEOTIDYLTRANSFERASE / NS3 HELICASE STRUCTURE / VIRION / ATPASE / NUCLEUS / MEMBRANE / SECRETED / ATP-BINDING / RNA-BINDING / FLAVIVIRUSES / GLYCOPROTEIN / RNA-DIRECTED RNA POLYMERASE / RNA REPLICATION / SERINE PROTEASE / ENVELOPE PROTEIN / DENGUE VIRUS / METAL-BINDING / TRANSMEMBRANE / TRANSCRIPTION / PHOSPHOPROTEIN / CAPSID PROTEIN | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel 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 / 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 | DENGUE VIRUS 4 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Luo, D.H. / Xu, T. / Watson, R.P. / Becker, D.S. / Sampath, A. / Jahnke, W. / Yeong, S.S. / Wang, C.H. / Lim, S.P. / Vasudevan, S.G. / Lescar, J. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein. Authors: Luo, D. / Xu, T. / Watson, R.P. / Scherer-Becker, D. / Sampath, A. / Jahnke, W. / Yeong, S.S. / Wang, C.H. / Lim, S.P. / Strongin, A. / Vasudevan, S.G. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jlr.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jlr.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jlr_validation.pdf.gz | 803.6 KB | Display | wwPDB validaton report |
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Full document | 2jlr_full_validation.pdf.gz | 811.6 KB | Display | |
Data in XML | 2jlr_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2jlr_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlr ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlr | HTTPS FTP |
-Related structure data
Related structure data | 2jlqSC 2jlsC 2jluC 2jlvC 2jlwC 2jlxC 2jlyC 2jlzC 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: 51353.473 Da / Num. of mol.: 1 / Fragment: RESIDUES 1646-2092 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: Q2YHF0, flavivirin |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.61 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.5 Å / Num. obs: 34139 / % possible obs: 93.6 % / Observed criterion σ(I): 1.3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.3 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JLQ Resolution: 2→19.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.949 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 33.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.65 Å
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Refine LS restraints |
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