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Yorodumi- PDB-2p1d: Crystal structure of dengue methyltransferase in complex with GTP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p1d | ||||||
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Title | Crystal structure of dengue methyltransferase in complex with GTP and S-Adenosyl-L-homocysteine | ||||||
Components | type II methyltransferase | ||||||
Keywords | VIRAL PROTEIN / TRANSFERASE / VIZIER / Viral Enzymes Involved in Replication / Dengue virus methyltransferase / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP / VIZIER. Viral Enzymes Involved in 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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / 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: 2.9 Å | ||||||
Authors | Egloff, M.P. / Benarooch, D. / Marseilles Structural Genomics Program @ AFMB (MSGP) | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: An RNA cap (nucleoside-2'-O)-methyltransferase in the flavivirus 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p1d.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p1d.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 2p1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1d ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1d | HTTPS FTP |
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-Related structure data
Related structure data | 1l9kSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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
#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.) Dengue virus 2 / Genus: Flavivirus / Species: Dengue virus / Strain: type 2 New Guinea / Gene: NSP5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS References: UniProt: Q9WLZ8, UniProt: P12823*PLUS, RNA-directed RNA polymerase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-5GP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.75 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.993 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.993 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 9322 / Num. obs: 9310 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 83.54 Å2 / Rsym value: 0.041 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1342 / Rsym value: 0.277 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L9K Resolution: 2.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: maximum likelihood
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Displacement parameters | Biso mean: 33.16 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.02 Å
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