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Yorodumi- PDB-5wz3: Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase(RdRP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wz3 | ||||||
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Title | Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase(RdRP) | ||||||
Components | NS5 RdRp | ||||||
Keywords | TRANSFERASE / Zika virus / NS5 / RdRp / RNA-dependent RNA polymerase | ||||||
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 / protein dimerization activity / symbiont entry into host cell ...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 / protein dimerization activity / 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 / 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 | Zika virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 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 | 5wz3.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wz3.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wz3 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wz3 | HTTPS FTP |
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-Related structure data
Related structure data | 5wz1C 5wz2C 2j7uS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 72075.039 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2795-3407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1B2ZC85, UniProt: A0A109PRQ3*PLUS | ||
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#2: Chemical | #3: 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: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 60.9 mM Tris (base), 39.1 mM Bicine, pH 8.5, 12 % v/v ethylene glycol and 6 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.72929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72929 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 61460 / % possible obs: 98.5 % / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Net I/σ(I): 22.098 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J7U Resolution: 1.804→34.159 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.804→34.159 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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