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- PDB-7oj4: Crystal structure of apo NS3 helicase from tick-borne encephaliti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oj4 | |||||||||
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Title | Crystal structure of apo NS3 helicase from tick-borne encephalitis virus | |||||||||
![]() | NS3 helicase domain | |||||||||
![]() | VIRAL PROTEIN / RNA helicase / hydrolase / non-structural protein | |||||||||
Function / homology | ![]() symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 / symbiont entry into host cell / 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 / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Anindita, P.D. / Havlickova, P. / Kascakova, B. / Grinkevich, P. / Brynda, J. / Franta, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic insight into the RNA-stimulated ATPase activity of tick-borne encephalitis virus helicase. Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z. #1: ![]() Title: Mechanistic insight into the ATP hydrolysis cycle of tick-borne encephalitis virus helicase Authors: Anindita, P.D. / Halbeisen, M. / Reha, D. / Tuma, R. / Franta, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185 KB | Display | ![]() |
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PDB format | ![]() | 140.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.5 KB | Display | ![]() |
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Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7blvC ![]() 7bm0C ![]() 7nxuC ![]() 6adwS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53489.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis Tris Propane pH 6.5, 0.2 M Sodium acetate trihydrate, 20% w/v PEG 3350, 10% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.828→49.06 Å / Num. obs: 48205 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 2.22 |
Reflection shell | Resolution: 1.83→1.94 Å / Num. unique obs: 7581 / CC1/2: 0.865 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ADW Resolution: 1.828→49.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.594 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.119 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.364 Å2
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Refinement step | Cycle: LAST / Resolution: 1.828→49.06 Å
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Refine LS restraints |
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LS refinement shell |
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