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Yorodumi- PDB-5z0r: Structural insight into the Zika virus capsid encapsulating the v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z0r | ||||||||||||
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Title | Structural insight into the Zika virus capsid encapsulating the viral genome | ||||||||||||
Components | Extracellular solute-binding protein family 1,viral genome protein | ||||||||||||
Keywords | VIRAL PROTEIN / Zika virus capsid | ||||||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex / ribonucleoside triphosphate phosphatase activity / cell chemotaxis / viral capsid / double-stranded RNA binding / outer membrane-bounded periplasmic space / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / periplasmic space / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont entry into host cell / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA damage response / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | 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 | China, 3items
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Citation | Journal: Cell Res. / Year: 2018 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z0r.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z0r.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 5z0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/5z0r ftp://data.pdbj.org/pub/pdb/validation_reports/z0/5z0r | HTTPS FTP |
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-Related structure data
Related structure data | 5z0vC 1ez9S 1sfkS 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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Unit cell |
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-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.) Escherichia coli (E. coli) / Strain: B / BL21-DE3, BL21(DE3) / Gene: ECBD_4002 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NCD0, UniProt: A0A1D9C0W3, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: 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: 2.3 Å3/Da / Density % sol: 46.63 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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Refine LS restraints |
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LS refinement shell |
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