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Yorodumi- PDB-2wzq: Insertion Mutant E173GP174 of the NS3 protease-helicase from deng... -
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-Basic information
Entry | Database: PDB / ID: 2wzq | ||||||
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Title | Insertion Mutant E173GP174 of the NS3 protease-helicase from dengue virus | ||||||
Components | (NS3 PROTEASE-HELICASE) x 2 | ||||||
Keywords | HYDROLASE / VIRION / TRANSMEMBRANE / ENVELOPE PROTEIN / NUCLEOTIDE-BINDING / CAPSID PROTEIN / DOMAIN MOBILITY / RNA REPLICATION | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Luo, D. / Wei, N. / Doan, D. / Paradkar, P. / Chong, Y. / Davidson, A. / Kotaka, M. / Lescar, J. / Vasudevan, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Flexibility between the Protease and Helicase Domains of the Dengue Virus Ns3 Protein Conferred by the Linker Region and its Functional Implications. Authors: Luo, D. / Wei, N. / Doan, D.N. / Paradkar, P.N. / Chong, Y. / Davidson, A.D. / Kotaka, M. / Lescar, J. / Vasudevan, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wzq.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wzq.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wzq_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 2wzq_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 2wzq_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2wzq_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wzq ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wzq | HTTPS FTP |
-Related structure data
Related structure data | 2whxC 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: 69576.250 Da / Num. of mol.: 1 / Fragment: RESIDUES 1475-1647,1648-2092 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2TN89, UniProt: Q2YHF0*PLUS |
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#2: Protein/peptide | Mass: 2897.053 Da / Num. of mol.: 1 / Fragment: RESIDUES 1393-1410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2TN89, UniProt: Q2YHF0*PLUS |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | CHAIN A INSERTION G174. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.51 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 17435 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VBC Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / SU B: 37.33 / SU ML: 0.344 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Displacement parameters | Biso mean: 24.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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