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- PDB-2p3l: Crystal Structure of Dengue Methyltransferase in Complex with Gpp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p3l | ||||||
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Title | Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine | ||||||
![]() | type II methyltransferase | ||||||
![]() | VIRAL PROTEIN / TRANSFERASE / VIZIER / Viral Enzymes Involved in Replication / Dengue virus methyltransferase / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP | ||||||
Function / homology | ![]() 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 / double-stranded RNA binding / viral capsid / 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 / double-stranded RNA binding / viral capsid / 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 / 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 / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Egloff, M.P. / Marseilles Structural Genomics Program @ AFMB (MSGP) | ||||||
![]() | ![]() Title: Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 Authors: Egloff, M.P. / Decroly, E. / Malet, H. / Selisko, B. / Benarroch, D. / Ferron, F. / 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 | ![]() | 73.9 KB | Display | ![]() |
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PDB format | ![]() | 52.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p3oC ![]() 2p3qC ![]() 2p40C ![]() 2p41C ![]() 1l9kS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34397.027 Da / Num. of mol.: 1 / Fragment: residues 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9WLZ8, UniProt: Q9WLZ5*PLUS, RNA-directed RNA polymerase |
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-Non-polymers , 6 types, 107 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/G3A.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/G3A.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-G3A / | #5: Chemical | ChemComp-CIT / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE DIFFERENCES BETWEEN THIS STRUCTURE AND UNP ENTRY Q9WLZ8_9FLAV REFLECT ACTUAL DIFFERENCES ...SEQUENCE DIFFERENCE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Nov 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.993 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. all: 19634 / Num. obs: 19614 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.91 Å2 / Rsym value: 0.061 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2825 / Rsym value: 0.382 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L9K Resolution: 2.2→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.111 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.367 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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