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Yorodumi- PDB-8a15: Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a15 | ||||||
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Title | Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2230 | ||||||
Components |
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Keywords | VIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / 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 / 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 ...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 / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / 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: 1.23 Å | ||||||
Authors | Huber, S. / Steinmetzer, T. | ||||||
Funding support | 1items
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Citation | Journal: Arch Pharm / Year: 2024 Title: Synthesis and structural characterization of new macrocyclic inhibitors of the Zika virus NS2B-NS3 protease. Authors: Huber, S. / Braun, N.J. / Schmacke, L.C. / Murra, R. / Bender, D. / Hildt, E. / Heine, A. / Steinmetzer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a15.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a15.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/8a15 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/8a15 | HTTPS FTP |
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-Related structure data
Related structure data | 7zpdC 7zq1C 7zqfC 7ztmC 7zumC 7zv4C 7zvvC 7zw5C 7zysC 8aqaC 8aqbC 8aqkC 5gpiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 5865.384 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q32ZE1 |
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#2: Protein | Mass: 19037.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase |
#3: Chemical | ChemComp-KPO / |
#4: 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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6 0.2 M ammonium sulfate 21% PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→42.24 Å / Num. obs: 71889 / % possible obs: 99.8 % / Redundancy: 6.51 % / Biso Wilson estimate: 15.66 Å2 / CC1/2: 0.999 / Rsym value: 0.048 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.23→1.3 Å / Redundancy: 6.39 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 11354 / CC1/2: 0.894 / Rsym value: 0.498 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GPI Resolution: 1.23→19.37 Å / SU ML: 0.0922 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.8938 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→19.37 Å
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Refine LS restraints |
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LS refinement shell |
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