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- PDB-2jly: Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jly | ||||||
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Title | Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate | ||||||
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![]() | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ENVELOPE PROTEIN / RIBONUCLEOPROTEIN / CAPSID PROTEIN / RNA REPLICATION / SERINE PROTEASE / GLYCOPROTEIN / DENGUE VIRUS / METAL-BINDING / TRANSFERASE / ATP-BINDING / RNA-BINDING / FLAVIVIRUSES / TRANSCRIPTION REGULATION / RNA-DIRECTED RNA POLYMERASE / NUCLEOTIDE-BINDING / VIRAL NUCLEOPROTEIN / SECRETED / HELICASE / PROTEASE / HYDROLASE / PHOSPHATE / CLEAVAGE ON PAIR OF BASIC RESIDUES / ENDOPLASMIC RETICULUM / NUCLEOTIDYLTRANSFERASE / ADP / SSRNA / VIRION / ATPASE / NUCLEUS / MEMBRANE / TRANSMEMBRANE / TRANSCRIPTION / PHOSPHOPROTEIN / NS3 HELICASE STRUCTURE / MULTIFUNCTIONAL ENZYME | ||||||
Function / homology | ![]() 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 / double-stranded RNA binding / viral capsid / 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 / double-stranded RNA binding / viral capsid / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209 KB | Display | ![]() |
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PDB format | ![]() | 162.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 55.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jlqC ![]() 2jlrC ![]() 2jlsC ![]() 2jluSC ![]() 2jlvC ![]() 2jlwC ![]() 2jlxC ![]() 2jlzC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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Components
-Protein / RNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 51337.453 Da / Num. of mol.: 2 / Fragment: RESIDUES 1646-2092 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | Mass: 3803.360 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 388 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.42 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40.8 Å / Num. obs: 188211 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JLU Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.87 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.548 / ESU R Free: 0.308 / 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: 35.621 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.99 Å
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Refine LS restraints |
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