+Open data
-Basic information
Entry | Database: PDB / ID: 5vim | ||||||
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Title | Crystal structure of the Zika virus NS5 methyltransferase. | ||||||
Components | Methyltransferase | ||||||
Keywords | VIRAL PROTEIN / methyltransferase / Zika virus | ||||||
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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / symbiont entry into host cell / 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 / 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: 2.1 Å | ||||||
Authors | Bukrejewska, M. / Derewenda, Z.S. / Derewenda, U. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain. Authors: Bukrejewska, M. / Derewenda, U. / Radwanska, M. / Engel, D.A. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vim.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vim.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5vim ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vim | HTTPS FTP |
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-Related structure data
Related structure data | 5vi7C 5kqrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29402.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192GPS6, UniProt: Q32ZE1*PLUS #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Lithium Sulfate, 0.1M Cacodylate, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 9, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.51 Å / Num. obs: 27143 / % possible obs: 97.1 % / Redundancy: 3.4 % / Net I/σ(I): 4.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KQR Resolution: 2.1→30.514 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.514 Å
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Refine LS restraints |
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LS refinement shell |
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