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Yorodumi- PDB-5yvv: Crystal structure of full length NS3 protein (gD4NS2BNS3) from DE... -
+Open data
-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 | |||||||||||||||
Components | (Genome polyprotein) x 2 | |||||||||||||||
Keywords | VIRAL PROTEIN / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / DEAH HELICASE / ATPASE / DENGUE VIRUS / FLAVIVIRUS | |||||||||||||||
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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / 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: 3.097 Å | |||||||||||||||
Authors | PHOO, W.W. / Sahili, A.E. | |||||||||||||||
Funding support | Singapore, 4items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yvv.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yvv.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yvv_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 5yvv_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 5yvv_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 5yvv_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yvv ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yvv | HTTPS FTP |
-Related structure data
Related structure data | 5yvjC 5yvuC 5yvwC 5yvyC 5yw1C 2vbcS 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: 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.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4, UniProt: Q2YHF0*PLUS |
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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.) Dengue virus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEL4, UniProt: Q2YHF0*PLUS |
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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