+Open data
-Basic information
Entry | Database: PDB / ID: 6ld5 | ||||||
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Title | Zika NS5 polymerase domain | ||||||
Components | RNA-directed RNA polymerase NS5 | ||||||
Keywords | TRANSFERASE / Zika Polymerase NS5 RdRP RNA depdendant RNA polymerase | ||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / 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 / 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 / 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 / centrosome / 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 / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | El Sahili, A. / Lescar, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: J.Virol. / Year: 2020 Title: Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase. Authors: Gharbi-Ayachi, A. / Santhanakrishnan, S. / Wong, Y.H. / Chan, K.W.K. / Tan, S.T. / Bates, R.W. / Vasudevan, S.G. / El Sahili, A. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ld5.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ld5.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 6ld5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/6ld5 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ld5 | HTTPS FTP |
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-Related structure data
Related structure data | 6ld1C 6ld2C 6ld3C 6ld4C 5tfrS 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: 74904.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A024B7W1, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-G8O / | #4: Chemical | ChemComp-G8L / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 10% PEG 6000, 0.2M HEPES pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.542 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→34.18 Å / Num. obs: 46894 / % possible obs: 95.88 % / Redundancy: 2.8 % / CC1/2: 0.981 / Rmerge(I) obs: 0.1362 / Net I/σ(I): 5.89 |
Reflection shell | Resolution: 1.94→2.01 Å / Rmerge(I) obs: 0.5432 / Num. unique obs: 4079 / CC1/2: 0.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TFR Resolution: 1.94→34.18 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.169 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.152
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→34.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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