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- PDB-6adm: Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Vi... -

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Basic information

Entry
Database: PDB / ID: 6adm
TitleAnthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions
Components
  • Anthrax toxin receptor 1
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Seneca Valley virus
Function / homology
Function and homology information


filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / Uptake and function of anthrax toxins / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / actin filament binding ...filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / Uptake and function of anthrax toxins / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / actin filament binding / transmembrane signaling receptor activity / channel activity / actin cytoskeleton organization / monoatomic ion transmembrane transport / RNA helicase activity / endosome membrane / external side of plasma membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / cell surface / proteolysis / RNA binding / ATP binding / 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 type A domain / Jelly Rolls - #20 / VWFA domain profile. ...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 type A domain / Jelly Rolls - #20 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / Picornavirus coat protein / 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 / Anthrax toxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Seneca valley virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou, Z.Y. / Cao, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
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.
History
DepositionAug 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.0Feb 6, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 6, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 6, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 6, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 6, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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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Assembly

Deposited unit
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9096
Polymers111,8855
Non-polymers241
Water00
1
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,714,535360
Polymers6,713,076300
Non-polymers1,45860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area19810 Å2
ΔGint-112 kcal/mol
Surface area39160 Å2
2


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


  • icosahedral pentamer
  • 560 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)559,54530
Polymers559,42325
Non-polymers1225
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
C: VP3
B: VP2
D: VP4
R: Anthrax toxin receptor 1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 671 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)671,45336
Polymers671,30830
Non-polymers1466
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

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Protein , 5 types, 5 molecules ACBDR

#1: Protein VP1


Mass: 28459.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#2: Protein VP3


Mass: 26296.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#3: Protein VP2


Mass: 29813.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#4: Protein VP4


Mass: 5998.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: A0A1U9IRU2
#5: Protein Anthrax toxin receptor 1 / Tumor endothelial marker 8


Mass: 21316.020 Da / Num. of mol.: 1 / Mutation: C177A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H6X2

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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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 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Seneca valley virus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.63 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9167 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097968
ELECTRON MICROSCOPYf_angle_d0.95410873
ELECTRON MICROSCOPYf_dihedral_angle_d10.2754703
ELECTRON MICROSCOPYf_chiral_restr0.0561191
ELECTRON MICROSCOPYf_plane_restr0.0081414

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