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- PDB-6adt: Structure of Seneca Valley Virus in neutral condition -

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Basic information

Entry
Database: PDB / ID: 6adt
TitleStructure of Seneca Valley Virus in neutral condition
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS
Function / homologyJelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesSeneca valley virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 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 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)92,1254
Polymers92,1254
Non-polymers00
Water00
1
A: VP1
C: VP3
B: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,527,508240
Polymers5,527,508240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area17950 Å2
ΔGint-104 kcal/mol
Surface area31960 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
x 5


  • icosahedral pentamer
  • 461 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)460,62620
Polymers460,62620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
C: VP3
B: VP2
D: VP4
x 6


  • icosahedral 23 hexamer
  • 553 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)552,75124
Polymers552,75124
Non-polymers00
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

#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

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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: all / 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: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11096 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0086425
ELECTRON MICROSCOPYf_angle_d0.8678795
ELECTRON MICROSCOPYf_dihedral_angle_d9.3473794
ELECTRON MICROSCOPYf_chiral_restr0.054974
ELECTRON MICROSCOPYf_plane_restr0.0081141

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