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Yorodumi- PDB-5kqr: Structure of NS5 methyltransferase from Zika virus bound to S-ade... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kqr | ||||||
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Title | Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine | ||||||
Components | Methyltransferase | ||||||
Keywords | TRANSFERASE / Zika / Flavivirus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / host cell surface / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / centrosome / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Zika virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.331 Å | ||||||
Authors | Jain, R. / Coloma, J. / Rajashankar, K.R. / Aggarwal, A.K. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Structures of NS5 Methyltransferase from Zika Virus. Authors: Coloma, J. / Jain, R. / Rajashankar, K.R. / Garcia-Sastre, A. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kqr.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kqr.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/5kqr ftp://data.pdbj.org/pub/pdb/validation_reports/kq/5kqr | HTTPS FTP |
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-Related structure data
Related structure data | 5kqsC 2px2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29538.742 Da / Num. of mol.: 1 / Fragment: MRNA cap 0-1 NS5-type MT residues 2521-2786 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A910, UniProt: A0A024B7W1*PLUS |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-CL / |
#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: 2.068 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 17-20% PEG 400, 0.1 M Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 50695 / % possible obs: 91.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.09 / % possible all: 55.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PX2 Resolution: 1.331→43.396 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.331→43.396 Å
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Refine LS restraints |
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LS refinement shell |
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