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- PDB-6adl: Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley V... -

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Basic information

Entry
Database: PDB / ID: 6adl
TitleAnthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions
Components
  • Anthrax toxin receptor 1
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / Seneca Valley 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 / 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 / Anthrax toxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Senecavirus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 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 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...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_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_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
A: VP1
C: VP3
B: VP2
R: Anthrax toxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1055
Polymers101,0814
Non-polymers241
Water00
1
A: VP1
C: VP3
B: VP2
R: Anthrax toxin receptor 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,066,329300
Polymers6,064,871240
Non-polymers1,45860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area14820 Å2
ΔGint-93 kcal/mol
Surface area36650 Å2
2


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


  • icosahedral pentamer
  • 506 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)505,52725
Polymers505,40620
Non-polymers1225
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
C: VP3
B: VP2
R: Anthrax toxin receptor 1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 607 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)606,63330
Polymers606,48724
Non-polymers1466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 25785.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1I9WAH6*PLUS
#2: Protein VP3


Mass: 26255.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1I9WAH6*PLUS
#3: Protein VP2


Mass: 27724.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: Q155Z9*PLUS
#4: Protein Anthrax toxin receptor 1 / Tumor endothelial marker 8


Mass: 21316.020 Da / Num. of mol.: 1 / Fragment: UNP residues 38-220 / Mutation: C177A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q9H6X2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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-#4 / Source: NATURAL
Source (natural)Organism: Seneca valley virus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3171 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077342
ELECTRON MICROSCOPYf_angle_d0.9110023
ELECTRON MICROSCOPYf_dihedral_angle_d10.1784337
ELECTRON MICROSCOPYf_chiral_restr0.0551095
ELECTRON MICROSCOPYf_plane_restr0.0071296

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