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

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Basic information

Entry
Database: PDB / ID: 6cx1
TitleCryo-EM structure of Seneca Valley Virus-Anthrax Toxin Receptor 1 complex
Components
  • Anthrax toxin receptor 1
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / Virus-receptor complex / Picornavirus / Senecavirus / Anthrax Toxin Receptor
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 / adhesion receptor-mediated virion attachment to host cell / filopodium membrane / 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 / adhesion receptor-mediated virion attachment to host cell / filopodium membrane / 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 / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / actin cytoskeleton organization / 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 / viral RNA genome replication / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / Jelly Rolls - #20 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain ...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 / Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Anthrax toxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Senecavirus A
MethodELECTRON MICROSCOPY / single 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.
History
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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  • Biological unit as icosahedral 23 hexamer
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Assembly

Deposited unit
E: Anthrax toxin receptor 1
A: Capsid protein VP1
C: Capsid protein VP2
B: Capsid protein VP3
D: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)111,7095
Polymers111,7095
Non-polymers00
Water00
1
E: Anthrax toxin receptor 1
A: Capsid protein VP1
C: Capsid protein VP2
B: Capsid protein VP3
D: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)6,702,561300
Polymers6,702,561300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Anthrax toxin receptor 1
A: Capsid protein VP1
C: Capsid protein VP2
B: Capsid protein VP3
D: Capsid protein VP4
x 5


  • icosahedral pentamer
  • 559 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)558,54725
Polymers558,54725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
E: Anthrax toxin receptor 1
A: Capsid protein VP1
C: Capsid protein VP2
B: Capsid protein VP3
D: Capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 670 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)670,25630
Polymers670,25630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Anthrax toxin receptor 1 / Tumor endothelial marker 8


Mass: 21026.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR1, ATR, TEM8 / Production host: Homo sapiens (human) / References: UniProt: Q9H6X2
#2: Protein Capsid protein VP1


Mass: 28459.969 Da / Num. of mol.: 1 / Fragment: residues 674-931 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2, UniProt: Q155Z9*PLUS
#3: Protein Capsid protein VP2


Mass: 29870.316 Da / Num. of mol.: 1 / Fragment: residues 162-429 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2, UniProt: Q155Z9*PLUS
#4: Protein Capsid protein VP3


Mass: 26353.938 Da / Num. of mol.: 1 / Fragment: residues 435-672 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2, UniProt: Q155Z9*PLUS
#5: Protein Capsid protein VP4


Mass: 5998.467 Da / Num. of mol.: 1 / Fragment: residues 93-150 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A218L148, UniProt: Q155Z9*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Seneca Valley Virus-Anthrax Toxin Receptor 1 complex / Type: VIRUS / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 6.5 MDa / Experimental value: NO
Source (natural)Organism: Senecavirus A
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellName: Capsid / Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
Buffer componentName: Phosphate Buffer
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: A homogenous sample containing full capsids
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Blot force 0, 3 sec blotting time

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 73000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 39 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7457
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6782 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00730699
ELECTRON MICROSCOPYf_angle_d1.19941983
ELECTRON MICROSCOPYf_dihedral_angle_d10.52718112
ELECTRON MICROSCOPYf_chiral_restr0.0674624
ELECTRON MICROSCOPYf_plane_restr0.0095465

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