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Yorodumi- PDB-5tfn: CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-op... -
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-Basic information
Entry | Database: PDB / ID: 5tfn | ||||||
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Title | CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation | ||||||
Components | NS2B-NS3 Protease CHIMERA,Genome polyprotein | ||||||
Keywords | VIRAL PROTEIN / Flavivirus / SERINE PROTEASE / 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 / double-stranded RNA binding / viral capsid / 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 / double-stranded RNA binding / viral capsid / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / 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 / viral envelope / lipid binding / 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: 3 Å | ||||||
Authors | Aleshin, A.E. / Bankston, L. / Liddington, R.C. | ||||||
Citation | Journal: To Be Published Title: A novel conformation for the Zika virus NS2B-NS3 protease offers new insights into biological regulation and inhibitor design. Authors: Aleshin, A.E. / Bankston, L. / Shiryaev, S.A. / Terskikh, A. / Strongin, A. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tfn.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tfn.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 5tfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tfn_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 5tfn_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 5tfn_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5tfn_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/5tfn ftp://data.pdbj.org/pub/pdb/validation_reports/tf/5tfn | HTTPS FTP |
-Related structure data
Related structure data | 5tfoC 2ijoS 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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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 50 - 1156 / Label seq-ID: 5 - 215
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-Components
#1: Protein | Mass: 25512.414 Da / Num. of mol.: 2 / Mutation: S135A Source method: isolated from a genetically manipulated source Details: Chains A and B were expressed as a single polypeptide chain., Chains A and B were expressed as a single polypeptide, connected by the artificial linker AGGGGSGGGGS Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A160JCU6, UniProt: Q32ZE1 #2: 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: 1.85 Å3/Da / Density % sol: 33.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→38.4 Å / Num. obs: 8410 / % possible obs: 99.8 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.71 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IJO Resolution: 3→38.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 61.084 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.109 Å2
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Refinement step | Cycle: 1 / Resolution: 3→38.4 Å
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Refine LS restraints |
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