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- EMDB-9608: Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-9608
TitleAnthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions
Map data
SampleSeneca valley virus:
virus / VP1 / VP3 / VP2 / VP4 / Anthrax toxin receptor 1 / ligand
Function / homology
Function and homology information


negative regulation of extracellular matrix assembly / reproductive process / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / actin cytoskeleton reorganization / T=pseudo3 icosahedral viral capsid ...negative regulation of extracellular matrix assembly / reproductive process / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / actin cytoskeleton reorganization / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / collagen binding / pore formation by virus in membrane of host cell / integral to membrane of host cell / transmembrane signaling receptor activity / actin filament binding / protein complex oligomerization / ion channel activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / endosome membrane / external side of plasma membrane / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / cell surface / RNA binding / membrane / integral component of membrane / ATP binding / plasma membrane / metal ion binding
von Willebrand factor, type A / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral ...von Willebrand factor, type A / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / Anthrax toxin receptor / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / von Willebrand factor A-like domain superfamily / Capsid protein VP4 superfamily, Picornavirus / Helicase, superfamily 3, single-stranded DNA/RNA virus
Genome polyprotein / Anthrax toxin receptor 1
Biological speciesSeneca valley virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 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: 6adm

SummaryFull reportAbout validation report
History
DepositionAug 1, 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-6adm
  • 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_9608.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 550 pix.
= 599.5 Å
1.09 Å/pix.
x 550 pix.
= 599.5 Å
1.09 Å/pix.
x 550 pix.
= 599.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.0569943 - 0.12408534
Average (Standard dev.)0.00106498 (±0.006466932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 599.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z599.500599.500599.500
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/NS550550550
D min/max/mean-0.0570.1240.001

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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: 7

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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: 28.459969 kDa
SourceSpecies: Seneca valley virus

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Component #3: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.296883 kDa
SourceSpecies: Seneca valley virus

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Component #4: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.813266 kDa
SourceSpecies: Seneca valley virus

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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.998467 kDa
SourceSpecies: Seneca valley virus

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Component #6: protein, Anthrax toxin receptor 1

ProteinName: Anthrax toxin receptor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.31602 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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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: 9167
3D reconstructionResolution: 2.84 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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