+Open data
-Basic information
Entry | Database: PDB / ID: 5gjc | ||||||
---|---|---|---|---|---|---|---|
Title | Zika virus NS3 helicase in complex with ATP | ||||||
Components | NS3 helicase | ||||||
Keywords | HYDROLASE / zika virus / helicase / ATP / Mn ion | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / 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 / 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: 2.204 Å | ||||||
Authors | Tian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. ...Tian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. / Xie, W. / Wang, Z.F. / Lou, H.Q. / Yang, H.T. / Rao, Z.H. | ||||||
Citation | Journal: Protein Cell / Year: 2016 Title: Structural basis of Zika virus helicase in recognizing its substrates Authors: Tian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. / Xie, W. / Wang, Z.F. / Lou, H.Q. / Yang, H.T. / Rao, Z.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gjc.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gjc.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gjc_validation.pdf.gz | 767.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5gjc_full_validation.pdf.gz | 770.1 KB | Display | |
Data in XML | 5gjc_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 5gjc_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/5gjc ftp://data.pdbj.org/pub/pdb/validation_reports/gj/5gjc | HTTPS FTP |
-Related structure data
Related structure data | 5gjbC 5jmtS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 49635.598 Da / Num. of mol.: 1 / Fragment: UNP residues 1682-2119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142DS38, UniProt: A0A0U4DG08*PLUS |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.4 Details: 0.1M HEPES(pH 7.4), 9% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 42724 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.942 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JMT Resolution: 2.204→37.729 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.12 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.204→37.729 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|