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Yorodumi- PDB-5wz2: Crystal structure of Zika virus NS5 methyltransferase bound to SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wz2 | ||||||
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Title | Crystal structure of Zika virus NS5 methyltransferase bound to SAM and RNA analogue (m7GpppA) | ||||||
Components | NS5 MTase | ||||||
Keywords | TRANSFERASE / Zika virus / methytransferase / RNA analogue / SAM | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural molecule activity / virion attachment to host cell / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Zika virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Duan, W. / Song, H. / Qi, J. / Shi, Y. / Gao, G.F. | ||||||
Citation | Journal: EMBO J. / Year: 2017 Title: The crystal structure of Zika virus NS5 reveals conserved drug targets. Authors: Duan, W. / Song, H. / Wang, H. / Chai, Y. / Su, C. / Qi, J. / Shi, Y. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wz2.cif.gz | 321.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wz2.ent.gz | 260.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wz2 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wz2 | HTTPS FTP |
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-Related structure data
Related structure data | 5wz1C 5wz3C 1l9kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30691.004 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 2525-2794 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A140E7U5, UniProt: A0A109PRQ3*PLUS #2: Chemical | #3: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24447 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.161 / Net I/σ(I): 9.362 |
Reflection shell | Resolution: 2.6→2.69 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L9K Resolution: 2.6→42.456 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→42.456 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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