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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 / homologyHelicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / von Willebrand factor, type A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular / Peptidase S1, PA clan ...Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / von Willebrand factor, type A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / RNA-directed RNA polymerase, catalytic domain / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Anthrax toxin receptor / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3A/C3B, picornaviral / Viral coat protein subunit / von Willebrand factor A-like domain superfamily / RNA helicase / Uptake and function of anthrax toxins / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / VWFA domain profile. / Anthrax receptor extracellular domain / Anthrax receptor C-terminus region / RNA dependent RNA polymerase / Capsid protein VP4 superfamily, Picornavirus / 3C cysteine protease (picornain 3C) / von Willebrand factor type A domain / picornavirus capsid protein / negative regulation of extracellular matrix assembly / reproductive process / icosahedral viral capsid / filopodium membrane / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / host cell cytoplasmic vesicle membrane / actin cytoskeleton reorganization / collagen binding / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / transmembrane signaling receptor activity / actin filament binding / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral entry into host cell / endosome membrane / cysteine-type endopeptidase activity / virion attachment to host cell / external side of plasma membrane / structural molecule activity / cell surface / RNA binding / transcription, DNA-templated / membrane / integral component of membrane / ATP binding / plasma membrane / metal ion binding / Genome polyprotein / Genome polyprotein / Anthrax toxin receptor 1
Function and homology information
Specimen sourceHomo sapiens (human)
Senecavirus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
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 Report
SummaryFull reportAbout validation report
DateDeposition: Apr 2, 2018 / Release: Oct 31, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 31, 2018Structure modelrepositoryInitial release
1.1Nov 14, 2018Structure modelData collection / Derived calculationspdbx_struct_oper_list_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]

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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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
Polyers111,7095
Non-polymers00
Water0
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
Polyers6,702,561300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers558,54725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers670,25630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

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


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


Mass: 28459.969 Da / Num. of mol.: 1 / Fragment: residues 674-931 / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2
#3: Protein/peptide Capsid protein VP2 /


Mass: 29870.316 Da / Num. of mol.: 1 / Fragment: residues 162-429 / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2
#4: Protein/peptide Capsid protein VP3 /


Mass: 26353.938 Da / Num. of mol.: 1 / Fragment: residues 435-672 / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2
#5: Protein/peptide Capsid protein VP4 /


Mass: 5998.467 Da / Num. of mol.: 1 / Fragment: residues 93-150 / Source: (natural) Senecavirus A / References: UniProt: A0A218L148

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Seneca Valley Virus-Anthrax Toxin Receptor 1 complex / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5 / Source: MULTIPLE SOURCES
Molecular weightValue: 6.5 MDa / Experimental value: NO
Source (natural)Organism: Senecavirus A
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus 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 / Details: A homogenous sample containing full capsids / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: Blot force 0, 3 sec blotting time

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 73000 / 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
4CTFFIND4.0CTF 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 selectionNumber of particles selected: 7457
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6782 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 100 / Ref protocol: RIGID BODY FIT / Ref 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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