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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


negative regulation of extracellular matrix assembly / reproductive process / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / actin cytoskeleton reorganization / collagen binding ...negative regulation of extracellular matrix assembly / reproductive process / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / actin cytoskeleton reorganization / collagen binding / transmembrane signaling receptor activity / actin filament binding / endosome membrane / external side of plasma membrane / cell surface / integral component of membrane / plasma membrane / metal ion binding
von Willebrand factor type A domain / von Willebrand factor A-like domain superfamily / Anthrax toxin receptor / Anthrax toxin receptor, extracellular domain / Anthrax toxin receptor, C-terminal / von Willebrand factor, type A / von Willebrand factor, type A domain / Jelly Rolls - #20 / Jelly Rolls / Sandwich ...von Willebrand factor type A domain / von Willebrand factor A-like domain superfamily / Anthrax toxin receptor / Anthrax toxin receptor, extracellular domain / Anthrax toxin receptor, C-terminal / von Willebrand factor, type A / von Willebrand factor, type A domain / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Anthrax toxin receptor 1
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release

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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)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
point symmetry operation60
Buried area19960 Å2
ΔGint-111 kcal/mol
Surface area39500 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
point symmetry operation5
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
point symmetry operation6
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 / Magnesium


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


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

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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 virusSenecavirus / Type: VIRUS / Entity ID: 1,2,3,4,5 / 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 FIELDBright-field microscopy
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

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0117965
f_angle_d1.01410871
f_dihedral_angle_d10.024699
f_chiral_restr0.061193
f_plane_restr0.0071412

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