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- PDB-5yvv: Crystal structure of full length NS3 protein (gD4NS2BNS3) from DE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yvv | |||||||||||||||
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Title | Crystal structure of full length NS3 protein (gD4NS2BNS3) from DENV4 in closed conformation | |||||||||||||||
![]() | (Genome polyprotein) x 2 | |||||||||||||||
![]() | VIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / ATPASE / DENGUE VIRUS / FLAVIVIRUS | |||||||||||||||
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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization ...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 / ribonucleoside triphosphate phosphatase 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 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 / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | PHOO, W.W. / Sahili, A.E. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain Authors: Phoo, W.W. / Sahili, A.E. / Zhang, Z.Z. / Chen, M.W. / Lescar, J. / Vasudevan, S. / Luo, D. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.5 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yvjC ![]() 5yvuC ![]() 5yvwC ![]() 5yvyC ![]() 5yw1C ![]() 2vbcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 67548.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1494-2092 / Mutation: L30S,F31S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 5745.130 Da / Num. of mol.: 1 / Fragment: UNP residues 1393-1439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
Sequence details | The structure is split in two chains due to the fact that one chain comes for the cofactor and the ...The structure is split in two chains due to the fact that one chain comes for the cofactor and the other from the NS3 protein. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.5, 12% PEG6000 / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→45.41 Å / Num. obs: 13710 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.07 / Rrim(I) all: 0.106 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2433 / CC1/2: 0.824 / Rpim(I) all: 0.375 / Rrim(I) all: 0.554 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vbc Resolution: 3.097→45.414 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.36 / 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: 3.097→45.414 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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