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Yorodumi- PDB-2jlx: Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Vanadate -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jlx | ||||||
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Title | Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Vanadate | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / 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 / VANADATE / PROTEASE / HYDROLASE / 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 | 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.H. / 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 | 2jlx.cif.gz | 210.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jlx.ent.gz | 164.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jlx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2jlx_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2jlx_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 2jlx_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlx ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlx | HTTPS FTP |
-Related structure data
Related structure data | 2jlqC 2jlrC 2jlsC 2jluSC 2jlvC 2jlwC 2jlyC 2jlzC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 2
NCS ensembles :
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-Components
-Protein / RNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 51365.527 Da / Num. of mol.: 2 / 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 #2: RNA chain | Mass: 3803.360 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 391 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.07 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.99 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→78.3 Å / Num. obs: 127207 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JLU Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.031 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.241 / 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: 21.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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