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- EMDB-9613: Structure of Seneca Valley Virus in neutral condition -

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Basic information

Entry
Database: EMDB / ID: EMD-9613
TitleStructure of Seneca Valley Virus in neutral condition
Map data
SampleSeneca valley virus:
virus / VP1 / VP3 / VP2 / VP4
Biological speciesSeneca valley virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLou ZY / Cao L
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1.
Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li ...Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao /
Abstract: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here we determine atomic structures of mature SVV particles alone and in complex with ANTXR1 in both neutral and acidic conditions, as well as empty "spent" particles in complex with ANTXR1 in acidic conditions by cryoelectron microscopy. SVV engages ANTXR1 mainly by the VP2 DF and VP1 CD loops, leading to structural changes in the VP1 GH loop and VP3 GH loop, which attenuate interprotomer interactions and destabilize the capsid assembly. Despite lying on the edge of the attachment site, VP2 D146 interacts with the metal ion in ANTXR1 and is required for cell entry. Though the individual substitution of most interacting residues abolishes receptor binding and virus propagation, a serine-to-alanine mutation at VP2 S177 significantly increases SVV proliferation. Acidification of the SVV-ANTXR1 complex results in a major reconfiguration of the pentameric capsid assemblies, which rotate ∼20° around the icosahedral fivefold axes to form a previously uncharacterized spent particle resembling a potential uncoating intermediate with remarkable perforations at both two- and threefold axes. These structures provide high-resolution snapshots of SVV entry, highlighting opportunities for anticancer therapeutic optimization.
Validation ReportPDB-ID: 6adt

SummaryFull reportAbout validation report
History
DepositionAug 2, 2018-
Header (metadata) releaseFeb 6, 2019-
Map releaseFeb 6, 2019-
UpdateFeb 6, 2019-
Current statusFeb 6, 2019Processing site: PDBj / 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
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6adt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9613.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 580 pix.
= 594.5 Å
1.03 Å/pix.
x 580 pix.
= 594.5 Å
1.03 Å/pix.
x 580 pix.
= 594.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.930.930.93
CCP4 map header1.0251.0251.025
EM Navigator Movie #11.0251.0251.025
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.034651123 - 0.08650931
Average (Standard dev.)0.00074389915 (±0.0041111014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 539.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0251.0251.025
M x/y/z580580580
origin x/y/z0.0000.0000.000
length x/y/z594.500594.500594.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS580580580
D min/max/mean-0.0350.0870.001

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Supplemental data

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Sample components

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Entire Seneca valley virus

EntireName: Seneca valley virus / Number of components: 5

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Component #1: virus, Seneca valley virus

VirusName: Seneca valley virusSenecavirus / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Seneca valley virus

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.494023 kDa
SourceSpecies: Seneca valley virus

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Component #3: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.393938 kDa
SourceSpecies: Seneca valley virus

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Component #4: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.843289 kDa
SourceSpecies: Seneca valley virus

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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.393875 kDa
SourceSpecies: Seneca valley virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 6
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.63 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 11096
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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