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- PDB-1r6a: Structure of the dengue virus 2'O methyltransferase in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r6a | ||||||
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Title | Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate | ||||||
![]() | Genome polyprotein | ||||||
![]() | TRANSFERASE / ribavirin 5'-triphosphate / dengue virus / 2'O methyltransferase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Benarroch, D. / Egloff, M.P. / Mulard, L. / Romette, J.L. / Canard, B. | ||||||
![]() | ![]() Title: A structural basis for the inhibition of the NS5 dengue virus mRNA 2'-O-methyltransferase domain by ribavirin 5'-triphosphate. Authors: Benarroch, D. / Egloff, M.P. / Mulard, L. / Guerreiro, C. / Romette, J.L. / Canard, B. #1: ![]() Title: An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirys RNA polymerase NS5:crystal structure and functional characterization Authors: EGLOFF, M.P. / BENARROCH, D. / SELISKO, B. / ROMETTE, J.L. / CANARD, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 955.2 KB | Display | ![]() |
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Full document | ![]() | 972.3 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33145.672 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase (residue 2492-2784) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Flavivirus / Species: Dengue virus / Strain: PR159-S1 / Gene: NS5 / Plasmid: pQE30 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-RVP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Na Citrate 0.1 M, AS 0.5 M, LiSO4 1.2 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 11869 / Num. obs: 11869 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.067 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.6→2.73 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.273 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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