|Entry||Database: PDB / ID: 6x2i|
|Title||The Cutavirus (CuV) capsid structure|
|Keywords||VIRUS / Icosahedral Capsid / Cutavirus / CuV / Protoparvovirus|
|Function / homology||Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1/VP2 / viral capsid / structural molecule activity / VP2|
Function and homology information
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å|
|Authors||Mietzsch, M. / Agbandje-McKenna, M.|
|Funding support|| United States, 1items |
|Citation||Journal: Viruses / Year: 2020|
Title: Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology.
Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria ...Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used ...Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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Mass: 61252.547 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutavirus / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1B0VEZ1
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Cutavirus / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Cutavirus|
|Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9|
|Details of virus||Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: unspecified|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 75 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: 1.10-2155_2155: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15296 / Symmetry type: POINT|
|Refine LS restraints|
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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