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Open data
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Basic information
Entry | Database: PDB / ID: 9.0E+41 | ||||||
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Title | Asymmetric unit of yPOWV | ||||||
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![]() | VIRAL PROTEIN | ||||||
Function / homology | ![]() ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||
![]() | Das, S. / Hafenstein, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Atomic-resolution structure of a chimeric Powassan tick-borne flavivirus. Authors: Sayan Das / Anoop Narayanan / Anqi Wang / Ibrahim M Moustafa / Sung Hyun Cho / Dana Mitzel / Joyce Jose / Susan L Hafenstein / ![]() Abstract: Powassan virus (POWV) is an emerging tick-borne flavivirus for which no vaccine or antiviral treatment exists. The incidence of human infections of POWV in North America has been increasing because ...Powassan virus (POWV) is an emerging tick-borne flavivirus for which no vaccine or antiviral treatment exists. The incidence of human infections of POWV in North America has been increasing because of the expanding distribution of the tick vector that transmits POWV to humans. To mitigate the dangers of handling a risk group 3 human pathogen, a chimeric virus was constructed from the genetic backbone of a yellow fever virus vaccine strain 17D (YFV-17D) and the external structural proteins of POWV lineage II. The chimera had a comparable phenotype as POWV. The atomic resolution of yellow fever virus-Powassan virus chimera (yPOWV) structure was built without ambiguity, revealing surface glycans and lipid pocket factors. The similarity to other flavivirus structures and the phenotype similar to YFV-17D suggest that there could be future potential as a vaccine candidate. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 619.2 KB | Display | ![]() |
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PDB format | ![]() | 521.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 60.9 KB | Display | |
Data in CIF | ![]() | 91.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 47497MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 53913.516 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 8418.004 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Chemical | ChemComp-CPL / Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Powassan virus / Type: VIRUS / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2177061 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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