[English] 日本語
![](img/lk-miru.gif)
- PDB-5z0r: Structural insight into the Zika virus capsid encapsulating the v... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5z0r | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structural insight into the Zika virus capsid encapsulating the viral genome | ||||||||||||
![]() | Extracellular solute-binding protein family 1,viral genome protein | ||||||||||||
![]() | VIRAL PROTEIN / Zika virus capsid | ||||||||||||
Function / homology | ![]() detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ribonucleoside triphosphate phosphatase activity ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ribonucleoside triphosphate phosphatase activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / double-stranded RNA binding / viral capsid / outer membrane-bounded periplasmic space / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / periplasmic space / 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 / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / DNA damage response / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. ...Li, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. / Ji, X. / Wang, Z. / Yang, H. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural insight into the Zika virus capsid encapsulating the viral genome. Authors: Li, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. / Ji, X. / Wang, Z. / Yang, H. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 190.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 54.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z0vC ![]() 1ez9S ![]() 1sfkS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 48977.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The fusion of MBP-TAG (UNP residues 27-395) and Zika virus capsid (UNP residues 24-98) Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A140NCD0, UniProt: A0A1D9C0W3, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 10% v/v 2-Propanol, 0.1 M BICINE pH 8.5, 30% w/v Polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97791 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 55737 / % possible obs: 94.7 % / Redundancy: 4.4 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.05→2.09 Å |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1EZ9, 1SFK Resolution: 2.05→48.286 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→48.286 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|