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- PDB-6adr: Anthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral... -

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Basic information

Entry
Database: PDB / ID: 6adr
TitleAnthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral conditions
Components
  • Anthrax toxin receptor 1
  • VP1
  • VP3
  • VP4
  • vp2
KeywordsVIRUS / Seneca Valley virus
Function / homology
Function and homology information


reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / actin filament binding / transmembrane signaling receptor activity ...reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / collagen binding / substrate adhesion-dependent cell spreading / actin filament binding / transmembrane signaling receptor activity / actin cytoskeleton organization / endosome membrane / external side of plasma membrane / cell surface / 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 / 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. / von Willebrand factor, type A ...Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / 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. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Anthrax toxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Seneca valley virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 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 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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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
D: VP4
R: Anthrax toxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4656
Polymers113,4415
Non-polymers241
Water181
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)6,807,927360
Polymers6,806,469300
Non-polymers1,45860
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area19960 Å2
ΔGint-111 kcal/mol
Surface area39500 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
  • 567 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)567,32730
Polymers567,20625
Non-polymers1225
Water905
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
  • 681 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)680,79336
Polymers680,64730
Non-polymers1466
Water1086
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: 28494.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
#2: Protein VP3


Mass: 26393.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
#3: Protein vp2


Mass: 29843.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
#4: Protein VP4


Mass: 7393.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus
#5: 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: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H6X2

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15460 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0117965
ELECTRON MICROSCOPYf_angle_d1.01410871
ELECTRON MICROSCOPYf_dihedral_angle_d10.024699
ELECTRON MICROSCOPYf_chiral_restr0.061193
ELECTRON MICROSCOPYf_plane_restr0.0071412

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