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- EMDB-3303: Cryo-EM reconstruction of Seneca VAlley Virus - receptor complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3303
TitleCryo-EM reconstruction of Seneca VAlley Virus - receptor complex
Map dataCryo-EM reconstruction of SVV-receptor complex
Sample
  • Sample: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex
  • Virus: Seneca valley virus
Biological speciesSeneca valley virus
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsMiles LA / Burga L / Bostina M / Poirier JT / Rudin CM
CitationJournal: J Clin Invest / Year: 2017
Title: Anthrax toxin receptor 1 is the cellular receptor for Seneca Valley virus.
Authors: Linde A Miles / Laura N Burga / Eric E Gardner / Mihnea Bostina / John T Poirier / Charles M Rudin /
Abstract: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. It has shown promise as a cancer therapeutic in preclinical studies and early-phase clinical ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. It has shown promise as a cancer therapeutic in preclinical studies and early-phase clinical trials. Here, we have identified anthrax toxin receptor 1 (ANTXR1) as the receptor for SVV using genome-wide loss-of-function screens. ANTXR1 is necessary for permissivity in vitro and in vivo. However, robust SVV replication requires an additional innate immune defect. We found that SVV interacts directly and specifically with ANTXR1, that this interaction is required for SVV binding to permissive cells, and that ANTXR1 expression is necessary and sufficient for infection in cell lines with decreased expression of antiviral IFN genes at baseline. Finally, we identified the region of the SVV capsid that is responsible for receptor recognition using cryoelectron microscopy of the SVV-ANTXR1-Fc complex. These studies identify ANTXR1, a class of receptor that is shared by a mammalian virus and a bacterial toxin, as the cellular receptor for SVV.
History
DepositionJan 21, 2016-
Header (metadata) releaseFeb 3, 2016-
Map releaseOct 11, 2017-
UpdateOct 11, 2017-
Current statusOct 11, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3303.png

Downloads & links

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Map

FileDownload / File: emd_3303.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of SVV-receptor complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.12 Å/pix.
x 180 pix.
= 561.6 Å		3.12 Å/pix.
x 180 pix.
= 561.6 Å		3.12 Å/pix.
x 180 pix.
= 561.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.00622528 - 0.13083661
Average (Standard dev.)0.00792713 (±0.02601571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin383838
Dimensions180180180
Spacing180180180
CellA=B=C: 561.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.123.123.12
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS383838
NC/NR/NS180180180
D min/max/mean-0.0060.1310.008

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Supplemental data

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Sample components

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Entire : Cryo-EM reconstruction of Seneca Valley Virus - receptor complex

EntireName: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex
Components
  • Sample: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex
  • Virus: Seneca valley virus

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Supramolecule #1000: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex

SupramoleculeName: Cryo-EM reconstruction of Seneca Valley Virus - receptor complex
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Seneca valley virus

SupramoleculeName: Seneca valley virus / type: virus / ID: 1 / NCBI-ID: 390157 / Sci species name: Seneca valley virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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

VitrificationCryogen name: ETHANE / Instrument: LEICA KF80

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Electron microscopy

MicroscopeJEOL 2200FS
DateOct 1, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 400 / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 400

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