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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 dataSeneca Valley Virus-Anthrax Toxin Receptor 1 complex
SampleSeneca Valley Virus-Anthrax Toxin Receptor 1 complex != Senecavirus A

Seneca Valley Virus-Anthrax Toxin Receptor 1 complex

  • Virus: Senecavirus A
    • Protein or peptide: Anthrax toxin receptor 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
KeywordsVirus-receptor complex / Picornavirus / Senecavirus / Anthrax Toxin Receptor / VIRUS
Function / homology
Function and homology information


reproductive process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host TRAF-mediated signal transduction / blood vessel development / lamellipodium membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity ...reproductive process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host TRAF-mediated signal transduction / blood vessel development / lamellipodium membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Uptake and function of anthrax toxins / collagen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / substrate adhesion-dependent cell spreading / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / actin filament binding / transmembrane signaling receptor activity / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / actin cytoskeleton organization / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / entry receptor-mediated virion attachment to host cell / RNA helicase activity / endosome membrane / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Picornavirus coat protein ...Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Picornavirus coat protein / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Anthrax toxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Senecavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJayawardena N / Burga L
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.
History
DepositionApr 2, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 31, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing 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 modelsPDB-6cx1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7772.png

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)
AnnotationSeneca Valley Virus-Anthrax Toxin Receptor 1 complex
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

Histogram

Histogram (log scale)
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
Components
  • Virus: Senecavirus A
    • Protein or peptide: Anthrax toxin receptor 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4

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Supramolecule #1: Senecavirus A

SupramoleculeName: Senecavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 390157 / Sci species name: Senecavirus A / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 6.5 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: Anthrax toxin receptor 1

MacromoleculeName: Anthrax toxin receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.026668 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CYGGFDLYFI LDKSGSVLHH WNEIYYFVEQ LAHKFISPQL RMSFIVFSTR GTTLMKLTED REQIRQGLEE LQKVLPGGDT YMHEGFERA SEQIYYENRQ GYRTASVIIA LTDGELHEDL FFYSEREANR SRDLGAIVYA VGVKDFNETQ LARIADSKDH V FPVNDGFQ ALQGIIHSIL KKSC

UniProtKB: Anthrax toxin receptor 1

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Macromolecule #2: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 28.459969 KDa
SequenceString: STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP ...String:
STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP RAFASKGGKV SFVLPWNSVS SVLPVRWGGA SKLSSATRGL PAHADWGTIY AFVPRPNEKK STAVKHVAVY IR YKNARAW CPSMLPFRSY K

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 29.870316 KDa
SequenceString: DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG ...String:
DRVTTQTAGN TAINTQSSLG VLCAYVEDPT KSDPPSSSTD QPTTTFTAID RWYTGRLNSW TKAVKTFSFQ AVPLPGAFLS RQGGLNGGA FTATLHRHFL MKCGWQVQVQ CNLTQFHQGA LLVAMVPETT LDVKPDGKAK SLQELNEEQW VEMSDDYRTG K NMPFQSLG TYYRPPNWTW GPNFINPYQV TVFPHQILNA RTSTSVDINV PYIGETPTQS SETQNSWTLL VMVLVPLDYK EG ATTDPEI TFSVRPTSPY FNGLRNRYTA G

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 26.353938 KDa
SequenceString: GPIPTAPREN SLMFLSTLPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFERVP EPVPASDTYV PYVAVPTQFD DRPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV ...String:
GPIPTAPREN SLMFLSTLPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFERVP EPVPASDTYV PYVAVPTQFD DRPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV VPYISPSDYR ETRAITNSVY SADGWFSLHK LTKITLPPDC PQSPCILFFA SAGEDYTLRL PVDCNPSYVF

UniProtKB: Genome polyprotein

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Macromolecule #5: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 5.998467 KDa
SequenceString:
RGNNGNMTFN YYANTYQNSV DFSTSSSASG AGPGNSRGGL AGLLTNFSGI LNPLGYLK

UniProtKB: Genome polyprotein

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Component - Name: Phosphate Buffer
GridModel: Quantifoil R1.2/1.3 / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0, 3 sec blotting time.
DetailsA homogenous sample containing full capsids

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7457
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3cji

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 6782
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 1 / Avg.num./class: 6782 / Software - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 100 / Target criteria: CC
Output model

PDB-6cx1:
Cryo-EM structure of Seneca Valley Virus-Anthrax Toxin Receptor 1 complex

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