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- EMDB-7110: Cryo-EM structure of Seneca Valley Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-7110
TitleCryo-EM structure of Seneca Valley Virus
Map dataSeneca Valley Virus
SampleSeneca Valley Virus != Senecavirus

Seneca Valley Virus

  • Virus: Senecavirus
Biological speciesSenecavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsStraus 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: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7110.png

Downloads & links

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Map

FileDownload / File: emd_7110.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSeneca Valley Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å		0.82 Å/pix.
x 640 pix.
= 524.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.037818767 - 0.06361229
Average (Standard dev.)-0.00077128806 (±0.004155754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z640640640
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/NS640640640
D min/max/mean-0.0380.064-0.001

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Supplemental data

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Sample components

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Entire : Seneca Valley Virus

EntireName: Seneca Valley Virus
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: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20949
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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