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- EMDB-7772: Cryo-EM structure of Seneca Valley Virus-Anthrax Toxin Receptor 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-7772
TitleCryo-EM structure of Seneca Valley Virus-Anthrax Toxin Receptor 1 complex
Map data
SampleSeneca Valley Virus-Anthrax Toxin Receptor 1 complex:
virus / Anthrax toxin receptor 1 / (Capsid protein ...Capsid) x 4
Function / homology
Function and homology information


suppression by virus of host RIG-I signaling pathway / negative regulation of extracellular matrix assembly / reproductive process / suppression by virus of host TBK1 activity / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host IRF7 activity / host cell nucleolus / T=3 icosahedral viral capsid / Lys48-specific deubiquitinase activity / Lys63-specific deubiquitinase activity ...suppression by virus of host RIG-I signaling pathway / negative regulation of extracellular matrix assembly / reproductive process / suppression by virus of host TBK1 activity / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host IRF7 activity / host cell nucleolus / T=3 icosahedral viral capsid / Lys48-specific deubiquitinase activity / Lys63-specific deubiquitinase activity / filopodium membrane / toxin transport / blood vessel development / suppression by virus of host IRF3 activity / positive regulation of metallopeptidase activity / suppression by virus of host TRAF activity / lamellipodium membrane / thiol-dependent ubiquitinyl hydrolase activity / substrate adhesion-dependent cell spreading / suppression by virus of host RIG-I activity / picornain 3C / ubiquitinyl hydrolase 1 / actin cytoskeleton reorganization / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / suppression by virus of host MAVS activity / host cell cytoplasmic vesicle membrane / collagen binding / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase / transmembrane signaling receptor activity / actin filament binding / protein complex oligomerization / RNA-directed RNA polymerase / 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
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor, type A / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Anthrax toxin receptor / Picornavirus capsid / P-loop containing nucleoside triphosphate hydrolase ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor, type A / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Anthrax toxin receptor / Picornavirus capsid / 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 / Peptidase C3A/C3B, picornaviral / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus
Genome polyprotein / Genome polyprotein / Genome polyprotein / Anthrax toxin receptor 1
Biological speciesSenecavirus A / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJayawardena N / Burga L / Easingwood R / Takizawa Y / Wolf M / Bostina M
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for anthrax toxin receptor 1 recognition by Seneca Valley Virus.
Authors: Nadishka Jayawardena / Laura N Burga / Richard A Easingwood / Yoshimasa Takizawa / Matthias Wolf / Mihnea Bostina /
Abstract: Recently, the use of oncolytic viruses in cancer therapy has become a realistic therapeutic option. Seneca Valley Virus (SVV) is a newly discovered picornavirus, which has earned a significant ...Recently, the use of oncolytic viruses in cancer therapy has become a realistic therapeutic option. Seneca Valley Virus (SVV) is a newly discovered picornavirus, which has earned a significant reputation as a potent oncolytic agent. Anthrax toxin receptor 1 (ANTXR1), one of the cellular receptors for the protective antigen secreted by , has been identified as the high-affinity cellular receptor for SVV. Here, we report the structure of the SVV-ANTXR1 complex determined by single-particle cryo-electron microscopy analysis at near-atomic resolution. This is an example of a shared receptor structure between a mammalian virus and a bacterial toxin. Our structure shows that ANTXR1 decorates the outer surface of the SVV capsid and interacts with the surface-exposed BC loop and loop II of VP1, "the puff" of VP2 and "the knob" of VP3. Comparison of the receptor-bound capsid structure with the native capsid structure reveals that receptor binding induces minor conformational changes in SVV capsid structure, suggesting the role of ANTXR1 as an attachment receptor. Furthermore, our results demonstrate that the capsid footprint on the receptor is not conserved in anthrax toxin receptor 2 (ANTXR2), thereby providing a molecular mechanism for explaining the exquisite selectivity of SVV for ANTXR1.
Validation ReportPDB-ID: 6cx1

SummaryFull reportAbout validation report
History
DepositionApr 2, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 31, 2018-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cx1
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6cx1
  • 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_7772.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 420 pix.
= 596.4 Å
1.42 Å/pix.
x 420 pix.
= 596.4 Å
1.42 Å/pix.
x 420 pix.
= 596.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.018
Minimum - Maximum-0.05108152 - 0.06383123
Average (Standard dev.)0.00009918771 (±0.004499039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 596.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z596.400596.400596.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0510.0640.000

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Supplemental data

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Sample components

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Entire Seneca Valley Virus-Anthrax Toxin Receptor 1 complex

EntireName: Seneca Valley Virus-Anthrax Toxin Receptor 1 complex / Number of components: 6

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Component #1: virus, Senecavirus A

VirusName: Senecavirus A / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 6.5 MDa
SpeciesSpecies: Senecavirus A
Shell #1Name of element: Capsid / Diameter: 300.0 Å / T number (triangulation number): 3

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Component #2: protein, Anthrax toxin receptor 1

ProteinName: Anthrax toxin receptor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.026668 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.459969 kDa
SourceSpecies: Senecavirus A

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Component #4: protein, Capsid protein VP2

ProteinName: Capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.870316 kDa
SourceSpecies: Senecavirus A

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Component #5: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.353938 kDa
SourceSpecies: Senecavirus A

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Component #6: protein, Capsid protein VP4

ProteinName: Capsid protein VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.998467 kDa
SourceSpecies: Senecavirus A

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Blot force 0, 3 sec blotting time.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 39 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 73000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3500.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 6782
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: CC / Refinement space: REAL / Overall bvalue: 100
Output model

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