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Yorodumi- PDB-6kr3: Crystal structure of Dengue virus nonstructural protein NS5 (form 2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kr3 | ||||||
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Title | Crystal structure of Dengue virus nonstructural protein NS5 (form 2) | ||||||
Components | Genome polyprotein | ||||||
Keywords | VIRAL PROTEIN / polymerase / methyltransferase | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / protein complex oligomerization / monoatomic ion channel activity / 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 endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / serine-type endopeptidase activity / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.931 Å | ||||||
Authors | Wu, J. / Lu, G. / Ye, H.Q. / Gong, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Plos Pathog. / Year: 2020 Title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase. Authors: Wu, J. / Ye, H.Q. / Zhang, Q.Y. / Lu, G. / Zhang, B. / Gong, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kr3.cif.gz | 344.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kr3.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 6kr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kr3_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6kr3_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6kr3_validation.xml.gz | 65.2 KB | Display | |
Data in CIF | 6kr3_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6kr3 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6kr3 | HTTPS FTP |
-Related structure data
Related structure data | 6kr2C 4k6mS 4v0qS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 104543.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q91H74 |
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-Non-polymers , 5 types, 75 molecules
#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-SAH / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % / Mosaicity: 0.343 ° |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 6.1 / Details: PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.93→60 Å / Num. obs: 63847 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 64.31 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.064 / Rrim(I) all: 0.153 / Χ2: 1.033 / Net I/σ(I): 6.1 / Num. measured all: 356093 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K6M, 4V0Q Resolution: 2.931→49.812 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.69 Å2 / Biso mean: 60.351 Å2 / Biso min: 22.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.931→49.812 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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