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Open data
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Basic information
Entry | Database: PDB / ID: 6h80 | ||||||
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Title | Dengue-RdRp3-inhibitor complex co-crystallisation | ||||||
![]() | Genome polyprotein | ||||||
![]() | VIRAL PROTEIN / Dengue virus / crystallization screen / RNA-dependent RNA polymerase / flavivirus / antiviral drug-discovery | ||||||
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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Talapatra, S.K. / Kozielski, F. | ||||||
![]() | ![]() Title: Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases. Authors: Riccio, F. / Talapatra, S.K. / Oxenford, S. / Angell, R. / Mazzon, M. / Kozielski, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 102.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464 KB | Display | ![]() |
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Full document | ![]() | 484.1 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h9rC ![]() 4hhjS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 73624.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Sri Lanka/1266/2000 / Tissue: 866768 / Gene: pol Production host: ![]() ![]() References: UniProt: Q6YMS4, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase | ||||
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#2: Chemical | ChemComp-5V5 / | ||||
#3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH 8.0, 20% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→52.7 Å / Num. obs: 39134 / % possible obs: 98.9 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.032 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.482 / CC1/2: 0.809 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HHJ Resolution: 2.3→52.7 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→52.7 Å
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Refine LS restraints |
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LS refinement shell |
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