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- EMDB-7111: Cryo-EM structure of Seneca Valley Virus procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-7111
TitleCryo-EM structure of Seneca Valley Virus procapsid
Map dataSeneca Valley Virus procapsid
SampleSeneca Valley Virus procapsid != Senecavirus

Seneca Valley Virus procapsid

  • Virus: Senecavirus
Biological speciesSenecavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsStrauss M / Jayawardena N / Bostina M
CitationJournal: J Virol / Year: 2018
Title: Cryo-Electron Microscopy Structure of Seneca Valley Virus Procapsid.
Authors: Mike Strauss / Nadishka Jayawardena / Eileen Sun / Richard A Easingwood / Laura N Burga / Mihnea Bostina /
Abstract: Seneca Valley virus (SVV), like some other members of the , forms naturally occurring empty capsids, known as procapsids. Procapsids have the same antigenicity as full virions, so they present an ...Seneca Valley virus (SVV), like some other members of the , forms naturally occurring empty capsids, known as procapsids. Procapsids have the same antigenicity as full virions, so they present an interesting possibility for the formation of stable virus-like particles. Interestingly, although SVV is a livestock pathogen, it has also been found to preferentially infect tumor cells and is being explored for use as a therapeutic agent in the treatment of small-cell lung cancers. Here we used cryo-electron microscopy to investigate the procapsid structure and describe the transition of capsid protein VP0 to the cleaved forms of VP4 and VP2. We show that the SVV receptor binds the procapsid, as evidence of its native antigenicity. In comparing the procapsid structure to that of the full virion, we also show that a cage of RNA serves to stabilize the inside surface of the virus, thereby making it more acid stable. Viruses are extensively studied to help us understand infection and disease. One of the by-products of some virus infections are the naturally occurring empty virus capsids (containing no genome), termed procapsids, whose function remains unclear. Here we investigate the structure and formation of the procapsids of Seneca Valley virus, to better understand how they form, what causes them to form, how they behave, and how we can make use of them. One potential benefit of this work is the modification of the procapsid to develop it for targeted delivery of therapeutics or to make a stable vaccine against SVV, which could be of great interest to the agricultural industry.
History
DepositionNov 8, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateApr 3, 2019-
Current statusApr 3, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7111.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSeneca Valley Virus procapsid
Voxel sizeX=Y=Z: 1.64 Å
Density
Contour LevelBy EMDB: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.03512934 - 0.09485291
Average (Standard dev.)0.0002632483 (±0.00883685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z524.800524.800524.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0350.0950.000

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Supplemental data

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Sample components

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Entire : Seneca Valley Virus procapsid

EntireName: Seneca Valley Virus procapsid
Components
  • Virus: Senecavirus

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Supramolecule #1: Senecavirus

SupramoleculeName: Senecavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 586425 / Sci species name: Senecavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3526
FSC plot (resolution estimation)

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