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- PDB-5tfo: CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE with a dele... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tfo | ||||||
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Title | CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE with a deletion V76-L86 in NS2b | ||||||
![]() | NS2B-NS3 Protease CHIMERA,NS2B-NS3 PROTEASE,NS2B-NS3 Protease CHIMERA | ||||||
![]() | VIRAL PROTEIN / Flavivirus / SERINE PROTEASE / Zika virus | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aleshin, A.E. / Bankston, L. / Liddington, R.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 195 KB | Display | ![]() |
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PDB format | ![]() | 158.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5tfnC ![]() 2ijoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24508.318 Da / Num. of mol.: 2 Mutation: V76-L86 substituted with GG,V76-L86 substituted with GG,V76-L86 substituted with GG Source method: isolated from a genetically manipulated source Details: Residues V76-L86 of NS2B were substituted with GG Chains A and B were expressed as a single polypeptide chain. Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q32ZE1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.87 % |
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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: ![]() ![]() ![]() |
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: 2.51→39.03 Å / Num. obs: 13989 / % possible obs: 98.1 % / Redundancy: 6.3 % / CC1/2: 0.921 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.51→2.61 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.827 / % possible all: 84.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ijo Resolution: 2.51→38.567 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→38.567 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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